Re: short reads format

From asims@bcgsc.ca Wed Jul 12 13:17:23 2006 Return-Path: X-Original-To: ssrformat@bcgsc.ca Delivered-To: ssrformat@bcgsc.ca Received: from xchange1.phage.bcgsc.ca (xchange1.bcgsc.bc.ca [10.9.208.35]) by mail.bcgsc.bc.ca (Postfix) with ESMTP id A0238F0002FB for ; Wed, 12 Jul 2006 13:17:23 -0700 (PDT) X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C6A5F0.2F7C05CF" Date: Wed, 12 Jul 2006 13:17:23 -0700 Message-ID: <86C6E520C12E52429ACBCB01546DF4D3E95CE5@xchange1.phage.bcgsc.ca> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: test Thread-Index: Acal8C9UCybyr37MQEmteetkhrgKkA== From: "Asim Siddiqui" To: X-Mailman-Approved-At: Wed, 12 Jul 2006 13:18:18 -0700 Subject: [Ssrformat] test X-BeenThere: ssrformat@mail.bcgsc.ca X-Mailman-Version: 2.1.3 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 12 Jul 2006 20:17:26 -0000 This is a multi-part message in MIME format. ------_=_NextPart_001_01C6A5F0.2F7C05CF Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable =20 =20 Best Regards, =20 Asim -------------------------------------------- Asim Siddiqui, Ph.D. Group Leader, Bioinformatics Genome Sciences Centre Suite 100 570 West 7th Avenue Vancouver, BC Canada V5Z 4S6 http://www.bcgsc.bc.ca =20 Tel 604-707-5802 Fax 604-877-6085 =20 =20 ------_=_NextPart_001_01C6A5F0.2F7C05CF Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Best Regards,

Asim

--------------------------------------------
Asim Siddiqui,=20 Ph.D.
Group Leader, Bioinformatics
Genome Sciences Centre
Suite = 100

570 West 7th Avenue

Vancouver, BC

Canada V5Z 4S6

http://www.bcgsc.bc.ca
Tel =20 604-707-5802
Fax 604-877-6085

------_=_NextPart_001_01C6A5F0.2F7C05CF-- From asims@bcgsc.ca Wed Jul 12 13:23:53 2006 Return-Path: X-Original-To: ssrformat@bcgsc.ca Delivered-To: ssrformat@bcgsc.ca Received: from xchange1.phage.bcgsc.ca (xchange1.bcgsc.bc.ca [10.9.208.35]) by mail.bcgsc.bc.ca (Postfix) with ESMTP id E0E8CF0002FB for ; Wed, 12 Jul 2006 13:23:53 -0700 (PDT) X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C6A5F1.18222093" Date: Wed, 12 Jul 2006 13:23:53 -0700 Message-ID: <86C6E520C12E52429ACBCB01546DF4D3E95CE7@xchange1.phage.bcgsc.ca> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: test2 Thread-Index: Acal8Rf2/d7fmKXvQOeW1KO+c+XZLg== From: "Asim Siddiqui" To: Cc: Subject: [Ssrformat] test2 X-BeenThere: ssrformat@mail.bcgsc.ca X-Mailman-Version: 2.1.3 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 12 Jul 2006 20:23:56 -0000 This is a multi-part message in MIME format. ------_=_NextPart_001_01C6A5F1.18222093 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable =20 =20 Best Regards, =20 Asim -------------------------------------------- Asim Siddiqui, Ph.D. Group Leader, Bioinformatics Genome Sciences Centre Suite 100 570 West 7th Avenue Vancouver, BC Canada V5Z 4S6 http://www.bcgsc.bc.ca =20 Tel 604-707-5802 Fax 604-877-6085 =20 =20 ------_=_NextPart_001_01C6A5F1.18222093 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Best Regards,

Asim

--------------------------------------------
Asim Siddiqui,=20 Ph.D.
Group Leader, Bioinformatics
Genome Sciences Centre
Suite = 100

570 West 7th Avenue

Vancouver, BC

Canada V5Z 4S6

http://www.bcgsc.bc.ca
Tel =20 604-707-5802
Fax 604-877-6085

------_=_NextPart_001_01C6A5F1.18222093-- From asims@bcgsc.ca Wed Jul 12 13:24:40 2006 Return-Path: X-Original-To: ssrformat@bcgsc.ca Delivered-To: ssrformat@bcgsc.ca Received: from xchange1.phage.bcgsc.ca (xchange1.bcgsc.bc.ca [10.9.208.35]) by mail.bcgsc.bc.ca (Postfix) with ESMTP id 1E74EF0002FE for ; Wed, 12 Jul 2006 13:24:40 -0700 (PDT) X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C6A5F1.33A78812" Date: Wed, 12 Jul 2006 13:24:39 -0700 Message-ID: <86C6E520C12E52429ACBCB01546DF4D3E95CE9@xchange1.phage.bcgsc.ca> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: test3 Thread-Index: Acal8TOA84rItguZQGKrEYrsF5IOZw== From: "Asim Siddiqui" To: Cc: Subject: [Ssrformat] test3 X-BeenThere: ssrformat@mail.bcgsc.ca X-Mailman-Version: 2.1.3 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 12 Jul 2006 20:24:42 -0000 This is a multi-part message in MIME format. ------_=_NextPart_001_01C6A5F1.33A78812 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable test =20 Best Regards, =20 Asim -------------------------------------------- Asim Siddiqui, Ph.D. Group Leader, Bioinformatics Genome Sciences Centre Suite 100 570 West 7th Avenue Vancouver, BC Canada V5Z 4S6 http://www.bcgsc.bc.ca =20 Tel 604-707-5802 Fax 604-877-6085 =20 =20 ------_=_NextPart_001_01C6A5F1.33A78812 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

test

Best Regards,

Asim

--------------------------------------------
Asim Siddiqui,=20 Ph.D.
Group Leader, Bioinformatics
Genome Sciences Centre
Suite = 100

570 West 7th Avenue

Vancouver, BC

Canada V5Z 4S6

http://www.bcgsc.bc.ca
Tel =20 604-707-5802
Fax 604-877-6085

------_=_NextPart_001_01C6A5F1.33A78812-- From asims@bcgsc.ca Wed Jul 12 14:07:15 2006 Return-Path: X-Original-To: ssrformat@bcgsc.ca Delivered-To: ssrformat@bcgsc.ca Received: from xchange1.phage.bcgsc.ca (xchange1.bcgsc.bc.ca [10.9.208.35]) by mail.bcgsc.bc.ca (Postfix) with ESMTP id A2AB7F00030E for ; Wed, 12 Jul 2006 14:07:15 -0700 (PDT) X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C6A5F7.26ADD645" Date: Wed, 12 Jul 2006 14:07:14 -0700 Message-ID: <86C6E520C12E52429ACBCB01546DF4D3E95CED@xchange1.phage.bcgsc.ca> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: short reads format Thread-Index: Acal9yZweiNGNma2QnWDxoxlWyQiaw== From: "Asim Siddiqui" To: "Steven Jones" , , , "Gabor Marth" , "Aaron Quinlan" , "Michael Stromberg" , "Avak Kahvejian" , "Du, Lei" , "James Bonfield" , , , "Rene Warren" , "Matthew Bainbridge" , X-Mailman-Approved-At: Thu, 13 Jul 2006 09:53:42 -0700 Cc: JSSadmin Subject: [Ssrformat] short reads format X-BeenThere: ssrformat@mail.bcgsc.ca X-Mailman-Version: 2.1.3 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 12 Jul 2006 21:07:18 -0000 This is a multi-part message in MIME format. ------_=_NextPart_001_01C6A5F7.26ADD645 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi, =20 You are receiving this e-mail because you have indicated an interest in developing a data format for short sequence reads. =20 As noted in my previous e-mail, the standard will be open and machine/platform independent. A mailing list (ssrformats@bcgsc.ca) has been created and you can sign up for the list here http://www.bcgsc.ca/mailman/listinfo/ssrformat =20 You will be contacted by JSSadmin@bcgsc.ca to determine your availability to participate in a teleconference. The teleconference will have to start sometime between 8am->8:30am PST to accommodate all participants. We will try to arrange it for the end of next week. Given the large number of participants, it may be difficult to get a time that everyone can agree on. We'll aim to get at least one person from each institute/company. =20 I've developed a tentative agenda below, but feel free to comment. Also this is intended to be an open group, so all are welcome. =20 Agenda =3D=3D=3D=3D=3D=3D =20 1. Introductions 2. Agreement of general aims and purpose of standard 3. Review of existing standards http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in NCBI ZTR format (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=3Dshow&f=3Dformats&m=3D= doc&s =3Dformats). 4. Is a new standard necessary/requirements for new standard Possible discussion points - human readable/something easily parsed by PERL ? - combining sequence and quality values ? - optionally referencing/utilizing existing ontologies for experiment definition ? - etc 5. (If required) Framework for creating and approving the standard/discussion of IEEE role 6. Assignment of action items / next steps =20 Best Regards, =20 Asim -------------------------------------------- Asim Siddiqui, Ph.D. Group Leader, Bioinformatics Genome Sciences Centre Suite 100 570 West 7th Avenue Vancouver, BC Canada V5Z 4S6 http://www.bcgsc.bc.ca =20 Tel 604-707-5802 Fax 604-877-6085 =20 =20 ------_=_NextPart_001_01C6A5F7.26ADD645 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi,

You = are receiving=20 this e-mail because you have indicated an interest in developing a data = format=20 for short sequence reads.

As = noted in my=20 previous e-mail, the standard will be open and machine/platform=20 independent.

A = mailing list (ssrformats@bcgsc.ca) has been = created and=20 you can sign up for the list here http://www.bcgsc.= ca/mailman/listinfo/ssrformat

You = will be=20 contacted by JSSadmin@bcgsc.ca = to=20 determine your availability to participate in a teleconference. The=20 teleconference will have to start sometime between 8am->8:30am PST to = accommodate all participants. We will try to arrange it for the end of = next=20 week. Given the large number of participants, it may be difficult to get = a time=20 that everyone can agree on. We'll aim to get at least one person from = each=20 institute/company.

I've = developed a=20 tentative agenda below, but feel free to comment. Also this is intended = to be an=20 open group, so all are welcome.

Agenda

=3D=3D=3D=3D=3D=3D

1.=20 Introductions

2. = Agreement of=20 general aims and purpose of standard

3. = Review of=20 existing standards

http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in

NCBI = ZTR format (http://www.ncbi.nlm.nih.gov/Traces/tr= ace.cgi?cmd=3Dshow&f=3Dformats&m=3Ddoc&s=3Dformats).

4. Is = a new standard=20 necessary/requirements for new standard

Possible discussion=20 points

- human=20 readable/something easily parsed by PERL ?

- combining=20 sequence and quality values ?

- optionally=20 referencing/utilizing existing ontologies for experiment definition=20 ?

-=20 etc

5. (If = required)=20 Framework for creating and approving the standard/discussion of=20 IEEE role

6. = Assignment of=20 action items / next steps

Best Regards,

Asim

--------------------------------------------
Asim Siddiqui,=20 Ph.D.
Group Leader, Bioinformatics
Genome Sciences Centre
Suite = 100

570 West 7th Avenue

Vancouver, BC

Canada V5Z 4S6

http://www.bcgsc.bc.ca
Tel =20 604-707-5802
Fax 604-877-6085

------_=_NextPart_001_01C6A5F7.26ADD645-- From JSSadmin@bcgsc.ca Wed Jul 12 14:21:11 2006 Return-Path: X-Original-To: ssrformat@bcgsc.ca Delivered-To: ssrformat@bcgsc.ca Received: from xchange1.phage.bcgsc.ca (xchange1.bcgsc.bc.ca [10.9.208.35]) by mail.bcgsc.bc.ca (Postfix) with ESMTP id CD7FFF00030D for ; Wed, 12 Jul 2006 14:21:10 -0700 (PDT) X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C6A5F9.18953DA6" Date: Wed, 12 Jul 2006 14:21:10 -0700 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: short reads format Thread-Index: Acal9yZweiNGNma2QnWDxoxlWyQiawAAThIw From: "JSSadmin" To: "Steven Jones" , , , "Gabor Marth" , "Aaron Quinlan" , "Michael Stromberg" , "Avak Kahvejian" , "Du, Lei" , "James Bonfield" , , , "Rene Warren" , "Matthew Bainbridge" , X-Mailman-Approved-At: Thu, 13 Jul 2006 09:53:42 -0700 Cc: Subject: [Ssrformat] RE: short reads format X-BeenThere: ssrformat@mail.bcgsc.ca X-Mailman-Version: 2.1.3 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 12 Jul 2006 21:21:13 -0000 This is a multi-part message in MIME format. ------_=_NextPart_001_01C6A5F9.18953DA6 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi all, =20 Please let me know which of the following timeslots is most convenient for you: =20 Thursday July 20th, 8:30-10:00am PST Friday July 21st, 8:30-10:00am PST =20 These are reserved as TBC in Asim's calendar. We could alternatively do a 8:00-9:30am PST timeslot, if that works better for everyone. =20 Thanks, Shallom Shallom Ly and Charlotte Watts=20 Administration to Dr. Steven Jones, Ms. Jacquie Schein and Dr. Asim Siddiqui=20 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency=20 jssadmin@bcgsc.ca=20 604.707.5900 x 5413 (Shallom)=20 604.707.5900 x 5473 (Charlotte)=20 ________________________________ From: Asim Siddiqui=20 Sent: Wednesday, July 12, 2006 2:07 PM To: Steven Jones; flicek@ebi.ac.uk; clive.Brown@solexa.com; Gabor Marth; 'Aaron Quinlan'; 'Michael Stromberg'; Avak Kahvejian; Du, Lei; James Bonfield; aleksey@ncbi.nlm.nih.gov; church@ncbi.nlm.nih.gov; Rene Warren; Matthew Bainbridge; ssrformat@bcgsc.ca Cc: JSSadmin Subject: short reads format Hi, =20 You are receiving this e-mail because you have indicated an interest in developing a data format for short sequence reads. =20 As noted in my previous e-mail, the standard will be open and machine/platform independent. A mailing list (ssrformats@bcgsc.ca) has been created and you can sign up for the list here http://www.bcgsc.ca/mailman/listinfo/ssrformat =20 You will be contacted by JSSadmin@bcgsc.ca to determine your availability to participate in a teleconference. The teleconference will have to start sometime between 8am->8:30am PST to accommodate all participants. We will try to arrange it for the end of next week. Given the large number of participants, it may be difficult to get a time that everyone can agree on. We'll aim to get at least one person from each institute/company. =20 I've developed a tentative agenda below, but feel free to comment. Also this is intended to be an open group, so all are welcome. =20 Agenda =3D=3D=3D=3D=3D=3D =20 1. Introductions 2. Agreement of general aims and purpose of standard 3. Review of existing standards http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in NCBI ZTR format (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=3Dshow&f=3Dformats&m=3D= doc&s =3Dformats). 4. Is a new standard necessary/requirements for new standard Possible discussion points - human readable/something easily parsed by PERL ? - combining sequence and quality values ? - optionally referencing/utilizing existing ontologies for experiment definition ? - etc 5. (If required) Framework for creating and approving the standard/discussion of IEEE role 6. Assignment of action items / next steps =20 Best Regards, =20 Asim -------------------------------------------- Asim Siddiqui, Ph.D. Group Leader, Bioinformatics Genome Sciences Centre Suite 100 570 West 7th Avenue Vancouver, BC Canada V5Z 4S6 http://www.bcgsc.bc.ca =20 Tel 604-707-5802 Fax 604-877-6085 =20 =20 ------_=_NextPart_001_01C6A5F9.18953DA6 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi all,

Please let me know which of the following = timeslots is most=20 convenient for you:

Thursday July 20th,=20 8:30-10:00am PST

Friday July 21st, = 8:30-10:00am PST

These are reserved as TBC in Asim's = calendar. We=20 could alternatively do a 8:00-9:30am PST timeslot, if that works better = for=20 everyone.

Thanks,
Shallom

Shallom=20 Ly and = Charlotte=20 Watts
Administration=20 to Dr. Steven Jones, Ms. Jacquie Schein and Dr. Asim = Siddiqui=20
Canada's Michael = Smith Genome=20 Sciences Centre, BC Cancer Agency
jssadmin@bcgsc.ca
604.707.5900 x 5413 (Shallom) =
604.707.5900 x 5473=20 (Charlotte)

From: Asim Siddiqui
Sent: = Wednesday,=20 July 12, 2006 2:07 PM
To: Steven Jones; flicek@ebi.ac.uk;=20 clive.Brown@solexa.com; Gabor Marth; 'Aaron Quinlan'; 'Michael = Stromberg'; Avak=20 Kahvejian; Du, Lei; James Bonfield; aleksey@ncbi.nlm.nih.gov;=20 church@ncbi.nlm.nih.gov; Rene Warren; Matthew Bainbridge;=20 ssrformat@bcgsc.ca
Cc: JSSadmin
Subject: short reads = format

Hi,

You = are receiving=20 this e-mail because you have indicated an interest in developing a data = format=20 for short sequence reads.

As = noted in my=20 previous e-mail, the standard will be open and machine/platform=20 independent.

A = mailing list (ssrformats@bcgsc.ca) has been = created and=20 you can sign up for the list here http://www.bcgsc.= ca/mailman/listinfo/ssrformat

I've = developed a=20 tentative agenda below, but feel free to comment. Also this is intended = to be an=20 open group, so all are welcome.

Agenda

=3D=3D=3D=3D=3D=3D

1.=20 Introductions

2. = Agreement of=20 general aims and purpose of standard

3. = Review of=20 existing standards

http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in

NCBI = ZTR format (http://www.ncbi.nlm.nih.gov/Traces/tr= ace.cgi?cmd=3Dshow&f=3Dformats&m=3Ddoc&s=3Dformats).

4. Is = a new standard=20 necessary/requirements for new standard

Possible discussion=20 points

- human=20 readable/something easily parsed by PERL ?

- combining=20 sequence and quality values ?

- optionally=20 referencing/utilizing existing ontologies for experiment definition=20 ?

-=20 etc

5. (If = required)=20 Framework for creating and approving the standard/discussion of=20 IEEE role

6. = Assignment of=20 action items / next steps

Best Regards,

Asim

--------------------------------------------
Asim Siddiqui,=20 Ph.D.
Group Leader, Bioinformatics
Genome Sciences Centre
Suite = 100

570 West 7th Avenue

Vancouver, BC

Canada V5Z 4S6

http://www.bcgsc.bc.ca
Tel =20 604-707-5802
Fax 604-877-6085

------_=_NextPart_001_01C6A5F9.18953DA6-- From aleksey@ncbi.nlm.nih.gov Thu Jul 13 08:44:58 2006 Return-Path: X-Original-To: ssrformat@bcgsc.ca Delivered-To: ssrformat@bcgsc.ca Received: from gotland.bcgsc.bc.ca (gotland.bcgsc.bc.ca [10.9.208.74]) by mail.bcgsc.bc.ca (Postfix) with ESMTP id 02976F00004D; Thu, 13 Jul 2006 08:44:58 -0700 (PDT) Received: from mailfwd.nih.gov (HELO nihrelayxway2.hub.nih.gov) ([128.231.90.107]) by gotland.bcgsc.bc.ca with ESMTP; 13 Jul 2006 08:44:57 -0700 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AQAAACIHtkSKOgIHBAoHBh0 X-IronPort-AV: i="4.06,238,1149490800"; d="scan'208"; a="187687:sNHT26395610" Received: from hera.ncbi.nlm.nih.gov ([130.14.25.41]) by nihrelayxway2.hub.nih.gov with ESMTP; 13 Jul 2006 11:44:56 -0400 X-IronPortListener: NIH_Relay X-SBRS: None X-IronPort-AV: i="4.06,238,1149480000"; d="scan'208"; a="182503231:sNHT34778576" Date: Thu, 13 Jul 2006 11:44:55 -0400 (EDT) From: Vladimir Alekseyev To: JSSadmin In-Reply-To: Message-ID: References: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Mailman-Approved-At: Thu, 13 Jul 2006 09:53:41 -0700 Cc: Matthew Bainbridge , trace@ncbi.nlm.nih.gov, Rene Warren , church@ncbi.nlm.nih.gov, clive.Brown@solexa.com, ssrformat@bcgsc.ca, Avak Kahvejian , Aaron Quinlan , Steven Jones , "Du, Lei" , Michael Stromberg , flicek@ebi.ac.uk, Gabor Marth Subject: [Ssrformat] RE: short reads format X-BeenThere: ssrformat@mail.bcgsc.ca X-Mailman-Version: 2.1.3 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 13 Jul 2006 15:45:00 -0000 Hi, Unfortunately I will not be able to make on July 20th. I have another meeting at that time. Friday suites me better. In case you decide to teleconference on Thursday then Dimitry Volodin will be communicating with you. He will be our main developer for this project. Thanks, Vladimir Alekseyev On Wed, 12 Jul 2006, JSSadmin wrote: > Hi all, > > Please let me know which of the following timeslots is most convenient > for you: > > Thursday July 20th, 8:30-10:00am PST > Friday July 21st, 8:30-10:00am PST > > These are reserved as TBC in Asim's calendar. We could alternatively do > a 8:00-9:30am PST timeslot, if that works better for everyone. > > Thanks, > Shallom > Shallom Ly and Charlotte Watts > Administration to Dr. Steven Jones, Ms. Jacquie Schein and Dr. Asim > Siddiqui > Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency > jssadmin@bcgsc.ca > 604.707.5900 x 5413 (Shallom) > 604.707.5900 x 5473 (Charlotte) > > ________________________________ > > From: Asim Siddiqui > Sent: Wednesday, July 12, 2006 2:07 PM > To: Steven Jones; flicek@ebi.ac.uk; clive.Brown@solexa.com; Gabor Marth; > 'Aaron Quinlan'; 'Michael Stromberg'; Avak Kahvejian; Du, Lei; James > Bonfield; aleksey@ncbi.nlm.nih.gov; church@ncbi.nlm.nih.gov; Rene > Warren; Matthew Bainbridge; ssrformat@bcgsc.ca > Cc: JSSadmin > Subject: short reads format > > > Hi, > > You are receiving this e-mail because you have indicated an interest in > developing a data format for short sequence reads. > > As noted in my previous e-mail, the standard will be open and > machine/platform independent. > A mailing list (ssrformats@bcgsc.ca) has been created and you can sign > up for the list here http://www.bcgsc.ca/mailman/listinfo/ssrformat > > You will be contacted by JSSadmin@bcgsc.ca to determine your > availability to participate in a teleconference. The teleconference will > have to start sometime between 8am->8:30am PST to accommodate all > participants. We will try to arrange it for the end of next week. Given > the large number of participants, it may be difficult to get a time that > everyone can agree on. We'll aim to get at least one person from each > institute/company. > > I've developed a tentative agenda below, but feel free to comment. Also > this is intended to be an open group, so all are welcome. > > Agenda > ====== > > 1. Introductions > 2. Agreement of general aims and purpose of standard > 3. Review of existing standards > http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in > NCBI ZTR format > (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s > =formats). > 4. Is a new standard necessary/requirements for new standard > Possible discussion points > - human readable/something easily parsed by PERL ? > - combining sequence and quality values ? > - optionally referencing/utilizing existing ontologies for experiment > definition ? > - etc > 5. (If required) Framework for creating and approving the > standard/discussion of IEEE role > 6. Assignment of action items / next steps > > > Best Regards, > > > > Asim > > -------------------------------------------- > Asim Siddiqui, Ph.D. > Group Leader, Bioinformatics > Genome Sciences Centre > Suite 100 > > 570 West 7th Avenue > > Vancouver, BC > > Canada V5Z 4S6 > > > http://www.bcgsc.bc.ca > Tel 604-707-5802 > Fax 604-877-6085 > > > > - Vladimir Alekseyev, NIH/NLM/NCBI Contractor From Clive.Brown@solexa.co.uk Fri Jul 14 06:56:21 2006 Return-Path: X-Original-To: ssrformat@bcgsc.ca Delivered-To: ssrformat@bcgsc.ca Received: from gotland.bcgsc.bc.ca (gotland.bcgsc.bc.ca [10.9.208.74]) by mail.bcgsc.bc.ca (Postfix) with ESMTP id ECEB0F000079; Fri, 14 Jul 2006 06:56:20 -0700 (PDT) Received: from smtp.nildram.co.uk ([195.112.4.54]) by gotland.bcgsc.bc.ca with ESMTP; 14 Jul 2006 06:56:20 -0700 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AQAAAO0+t0SCRDaHQgIHAgwFCB0 X-IronPort-AV: i="4.06,243,1149490800"; d="scan'208,217"; a="190946:sNHT46464780" Received: from mx1.frog.co.uk (mx1.frog.co.uk [84.12.255.26]) by smtp.nildram.co.uk (Postfix) with ESMTP id BDD49237BF2; Fri, 14 Jul 2006 14:56:00 +0100 (BST) X-SEF-Processed: 5_0_0_910__2006_07_14_14_56_02 Received: from Unknown [217.33.195.20] by mx1.frog.co.uk - SurfControl E-mail Filter (5.2.1); Fri, 14 Jul 2006 14:56:01 +0100 Received: from 192.168.34.111 ([192.168.34.111]) by solexchuk1.solexa.co.uk ([192.168.34.241]) with Microsoft Exchange Server HTTP-DAV ; Fri, 14 Jul 2006 13:56:17 +0000 User-Agent: Microsoft-Entourage/11.2.5.060620 Date: Fri, 14 Jul 2006 14:57:08 +0100 From: "Clive G. Brown User" To: JSSadmin , Steven Jones , , Gabor Marth , Aaron Quinlan , Michael Stromberg , Avak Kahvejian , "Du, Lei" , James Bonfield , , , Rene Warren , Matthew Bainbridge , Message-ID: Thread-Topic: short reads format Thread-Index: Acal9yZweiNGNma2QnWDxoxlWyQiawAAThIwAFVBo08= In-Reply-To: Mime-version: 1.0 Content-type: multipart/alternative; boundary="B_3235733829_1200333" X-Mailman-Approved-At: Fri, 14 Jul 2006 12:19:19 -0700 Cc: Subject: [Ssrformat] Re: short reads format X-BeenThere: ssrformat@mail.bcgsc.ca X-Mailman-Version: 2.1.3 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 14 Jul 2006 13:56:23 -0000 > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3235733829_1200333 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-NAIMIME-Disclaimer: 1 X-NAIMIME-Modified: 1 I (We) can do either ... Many thanks for pushing this along C. -- Clive G. Brown Director of Bioinformatics & I.T. Solexa Ltd. Chesterford Research Park Saffron Walden Essex UK CB10 1XL +44(0)1799 532300 http://www.solexa.com/ From: JSSadmin Date: Wed, 12 Jul 2006 22:21:10 +0100 To: Steven Jones , , Clive Brown , Gabor Marth , Aaron Quinlan , Michael Stromberg , Avak Kahvejian , "Du, Lei" , James Bonfield , , , Rene Warren , Matthew Bainbridge , Cc: Asim Siddiqui Conversation: short reads format Subject: RE: short reads format Hi all, Please let me know which of the following timeslots is most convenient for you: Thursday July 20th, 8:30-10:00am PST Friday July 21st, 8:30-10:00am PST These are reserved as TBC in Asim's calendar. We could alternatively do a 8:00-9:30am PST timeslot, if that works better for everyone. Thanks, Shallom Shallom Ly and Charlotte Watts Administration to Dr. Steven Jones, Ms. Jacquie Schein and Dr. Asim Siddiqui Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency jssadmin@bcgsc.ca 604.707.5900 x 5413 (Shallom) 604.707.5900 x 5473 (Charlotte) From: Asim Siddiqui Sent: Wednesday, July 12, 2006 2:07 PM To: Steven Jones; flicek@ebi.ac.uk; clive.Brown@solexa.com; Gabor Marth; 'Aaron Quinlan'; 'Michael Stromberg'; Avak Kahvejian; Du, Lei; James Bonfield; aleksey@ncbi.nlm.nih.gov; church@ncbi.nlm.nih.gov; Rene Warren; Matthew Bainbridge; ssrformat@bcgsc.ca Cc: JSSadmin Subject: short reads format Hi, You are receiving this e-mail because you have indicated an interest in developing a data format for short sequence reads. As noted in my previous e-mail, the standard will be open and machine/platform independent. A mailing list (ssrformats@bcgsc.ca) has been created and you can sign up for the list here http://www.bcgsc.ca/mailman/listinfo/ssrformat You will be contacted by JSSadmin@bcgsc.ca to determine your availability to participate in a teleconference. The teleconference will have to start sometime between 8am->8:30am PST to accommodate all participants. We will try to arrange it for the end of next week. Given the large number of participants, it may be difficult to get a time that everyone can agree on. We'll aim to get at least one person from each institute/company. I've developed a tentative agenda below, but feel free to comment. Also this is intended to be an open group, so all are welcome. Agenda ====== 1. Introductions 2. Agreement of general aims and purpose of standard 3. Review of existing standards http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in NCBI ZTR format (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=for mats ). 4. Is a new standard necessary/requirements for new standard Possible discussion points - human readable/something easily parsed by PERL ? - combining sequence and quality values ? - optionally referencing/utilizing existing ontologies for experiment definition ? - etc 5. (If required) Framework for creating and approving the standard/discussion of IEEE role 6. Assignment of action items / next steps Best Regards, Asim -------------------------------------------- Asim Siddiqui, Ph.D. Group Leader, Bioinformatics Genome Sciences Centre Suite 100 570 West 7th Avenue Vancouver, BC Canada V5Z 4S6 http://www.bcgsc.bc.ca Tel 604-707-5802 Fax 604-877-6085 The information in this email transmission and any files transmitted with it are intended solely for the use of the individual or entity to which they are addressed and may contain confidential and privileged information. Any third party dissemination, distribution, copying or use of this communication, without prior permission, is strictly prohibited. Any attachments may contain viruses that could damage your computer. While we have taken every reasonable precaution to minimise this risk, we cannot accept liability for such damage and you should carry out your own virus checks before opening any attachments. If you have received this email in error please notify the sender as soon as possible and delete all copies of this email. Copyright (C): 2006 By Solexa Ltd. All Rights Reserved. --B_3235733829_1200333 Content-type: text/HTML; charset="us-ascii" Content-transfer-encoding: quoted-printable X-NAIMIME-Disclaimer: 1 X-NAIMIME-Modified: 1 Re: short reads format I (We) can do either ...

Many thanks for pushing this along

C.
--
Clive G. Brown
Director of Bioinformatics & I.T.
Solexa Ltd.
Chesterford Research Park
Saffron Walden
Essex
UK
CB10 1XL

+44(0)1799 532300
http://www.solexa.com/

From: JSSadmin <JSS= admin@bcgsc.ca>
Date: Wed, 12 Jul 2006 22:21:10 +0100
To: Steven Jones <sjones@bcgsc.ca>, <flicek@ebi.ac.uk>= , Clive Brown <clive.Brown@solexa.com>, Gabor Marth <marth@bc.ed= u>, Aaron Quinlan <quinlaaa@bc.edu>, Michael Stromberg <mikae= ls@bc.edu>, Avak Kahvejian <akahvejian@helicosbio.com>, "Du= , Lei" <ldu@454.com>, James Bonfield <jkb@sanger.ac.uk>,= <aleksey@ncbi.nlm.nih.gov>, <church@ncbi.nlm.nih.gov>, Rene = Warren <rwarren@bcgsc.ca>, Matthew Bainbridge <matthewb@bcgsc.ca= >, <ssrformat@bcgsc.ca>
Cc: Asim Siddiqui <asims@bcgsc.ca>
Conversation: short reads format
Subject: RE: short reads format

Hi all,

Please let me know wh= ich of the following timeslots is most convenient for you:

Thursday July 20th, 8= :30-10:00am PST
Friday July 21st, 8:30-10:00am PST

These are reserved as= TBC in Asim's calendar. We could alternatively do a 8:00-9:30am PS= T timeslot, if that works better for everyone.

Thanks,
Shallom
Shallom Ly and Charlotte Watts
Administration to Dr. Steven Jones, Ms. Jacqu= ie Schein and Dr. Asim Siddiqui
Canada's Michael Smith Genome Sciences Centre= , BC Cancer Agency
jssadmin@bcgsc.ca
604.707.5900 x 5413 (Shallom)
604.707.5900 x 5473 (Charlotte)

From: Asim Siddiqui
Sent: Wednesday, July 12, 2006 2:07 PM
To: Steven Jones; flicek@ebi.ac.uk; clive.Brown@solexa.com; Gabor = Marth; 'Aaron Quinlan'; 'Michael Stromberg'; Avak Kahvejian; Du, Lei; Jam= es Bonfield; aleksey@ncbi.nlm.nih.gov; church@ncbi.nlm.nih.gov; Rene Warr= en; Matthew Bainbridge; ssrformat@bcgsc.ca
Cc: JSSadmin
Subject: short reads format

Hi,

You are receiving this e-mail because you hav= e indicated an interest in developing a data format for short sequence re= ads.

As noted in my previous e-mail, the standard = will be open and machine/platform independent.
A mailing list (ssrformats@bcgsc.ca) has been created and you can sign up= for the list here http://www.bcgsc.ca/mailman/listinfo/ssrformat

You will be contacted by JSSadmin@bcgsc.ca to= determine your availability to participate in a teleconference. The tele= conference will have to start sometime between 8am->8:30am PST to acco= mmodate all participants. We will try to arrange it for the end of next w= eek. Given the large number of participants, it may be difficult to get a= time that everyone can agree on. We'll aim to get at least one person fr= om each institute/company.

I've developed a tentative agenda below, but = feel free to comment. Also this is intended to be an open group, so all a= re welcome.

Agenda
=3D=3D=3D=3D=3D=3D

1. Introductions
2. Agreement of general aims and purpose of standard
3. Review of existing standards
http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in
NCBI ZTR format (http://www.ncbi.nlm.nih.gov/T= races/trace.cgi?cmd=3Dshow&f=3Dformats&m=3Ddoc&s=3Dformats <http://www.ncbi.nlm.nih.gov/= Traces/trace.cgi?cmd=3Dshow&f=3Dformats&m=3Ddoc&s= =3Dformats> ).
4. Is a new standard necessary/requirements for new standard
Possible discussion points
- human readable/something easily parsed by PERL ?
- combining sequence and quality values ?
- optionally referencing/utilizing existing ontologies for experime= nt definition ?
- etc
5. (If required) Framework for creating and approving the standard/discus= sion of IEEE role
6. Assignment of action items / next steps

Best Regards,

Asim

--------------------------------------------<= BR> Asim Siddiqui, Ph.D.
Group Leader, Bioinformatics
Genome Sciences Centre
Suite 100

570 West 7th Avenue

Vancouver, BC

Canada V5Z 4S6

http://www.bcgsc.bc.ca = <http://www.bcgsc.bc.ca/>
Tel 604-707-5802
Fax 604-877-6085

The information in this email transmission and any files transmitted with= it are intended solely for the use of the individual or entity to which = they are addressed and may contain confidential and privileged informatio= n. Any third party dissemination, distribution, copying or use of this co= mmunication, without prior permission, is strictly prohibited. Any attach= ments may contain viruses that could damage your computer. While we have = taken every reasonable precaution to minimise this risk, we cannot accept= liability for such damage and you should carry out your own virus checks= before opening any attachments. If you have received this email in error= please notify the sender as soon as possible and delete all copies of th= is email.
=0A
=0ACopyright (C): 2006 By Solexa Ltd. All Rights Rese= rved.

--B_3235733829_1200333-- From JSSadmin@bcgsc.ca Fri Jul 14 16:17:07 2006 Return-Path: X-Original-To: ssrformat@bcgsc.ca Delivered-To: ssrformat@bcgsc.ca Received: from xchange1.phage.bcgsc.ca (xchange1.bcgsc.bc.ca [10.9.208.35]) by mail.bcgsc.bc.ca (Postfix) with ESMTP id 39260F0002E4 for ; Fri, 14 Jul 2006 16:17:07 -0700 (PDT) X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Date: Fri, 14 Jul 2006 16:17:06 -0700 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: short reads format Thread-Index: Acamk0xJw4YN2PSWSRycJvCTji2MigBB08Ww From: "JSSadmin" To: "Vladimir Alekseyev" X-Mailman-Approved-At: Fri, 14 Jul 2006 17:06:12 -0700 Cc: Matthew Bainbridge , trace@ncbi.nlm.nih.gov, Rene Warren , church@ncbi.nlm.nih.gov, clive.Brown@solexa.com, ssrformat@bcgsc.ca, Avak Kahvejian , Aaron Quinlan , Steven Jones , "Du, Lei" , Michael Stromberg , flicek@ebi.ac.uk, Gabor Marth Subject: [Ssrformat] RE: short reads format X-BeenThere: ssrformat@mail.bcgsc.ca X-Mailman-Version: 2.1.3 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 14 Jul 2006 23:17:10 -0000 Hi all, With the exception of Vladmir, everyone who has replied is available on both dates. Therefore, I would like to confirm the teleconference date for Friday July 21st from 8:00-9:30am PST. If there is anyone who cannot make this time/date, please let me know. =20 For GSC participants, the 5th floor boardroom (Echelon) has been booked for your use. The room is reserved until 10am PST, just in case your meeting runs overtime. =20 For those of you calling in from other locations, I will be sending out an email on Monday with call-in details. Thanks, Shallom Shallom Ly and Charlotte Watts Administration to Dr. Steven Jones, Ms. Jacquie Schein and Dr. Asim Siddiqui Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency jssadmin@bcgsc.ca 604.707.5900 x 5413 (Shallom)=20 604.707.5900 x 5473 (Charlotte) -----Original Message----- From: Vladimir Alekseyev [mailto:aleksey@ncbi.nlm.nih.gov]=20 Sent: Thursday, July 13, 2006 8:45 AM To: JSSadmin Cc: Steven Jones; flicek@ebi.ac.uk; clive.Brown@solexa.com; Gabor Marth; Aaron Quinlan; Michael Stromberg; Avak Kahvejian; Du, Lei; James Bonfield; church@ncbi.nlm.nih.gov; Rene Warren; Matthew Bainbridge; ssrformat@bcgsc.ca; Asim Siddiqui; trace@ncbi.nlm.nih.gov Subject: RE: short reads format Hi, Unfortunately I will not be able to make on July 20th. I have another meeting at that time. Friday suites me better. In case you decide to teleconference on Thursday then Dimitry Volodin will be communicating with you. He will be our main developer for this project. Thanks, Vladimir Alekseyev On Wed, 12 Jul 2006, JSSadmin wrote: > Hi all, > > Please let me know which of the following timeslots is most convenient > for you: > > Thursday July 20th, 8:30-10:00am PST > Friday July 21st, 8:30-10:00am PST > > These are reserved as TBC in Asim's calendar. We could alternatively=20 > do a 8:00-9:30am PST timeslot, if that works better for everyone. > > Thanks, > Shallom > Shallom Ly and Charlotte Watts > Administration to Dr. Steven Jones, Ms. Jacquie Schein and Dr. Asim=20 > Siddiqui Canada's Michael Smith Genome Sciences Centre, BC Cancer=20 > Agency jssadmin@bcgsc.ca 604.707.5900 x 5413 (Shallom) 604.707.5900 x=20 > 5473 (Charlotte) > > ________________________________ > > From: Asim Siddiqui > Sent: Wednesday, July 12, 2006 2:07 PM > To: Steven Jones; flicek@ebi.ac.uk; clive.Brown@solexa.com; Gabor=20 > Marth; 'Aaron Quinlan'; 'Michael Stromberg'; Avak Kahvejian; Du, Lei;=20 > James Bonfield; aleksey@ncbi.nlm.nih.gov; church@ncbi.nlm.nih.gov;=20 > Rene Warren; Matthew Bainbridge; ssrformat@bcgsc.ca > Cc: JSSadmin > Subject: short reads format > > > Hi, > > You are receiving this e-mail because you have indicated an interest=20 > in developing a data format for short sequence reads. > > As noted in my previous e-mail, the standard will be open and=20 > machine/platform independent. > A mailing list (ssrformats@bcgsc.ca) has been created and you can sign > up for the list here http://www.bcgsc.ca/mailman/listinfo/ssrformat > > You will be contacted by JSSadmin@bcgsc.ca to determine your=20 > availability to participate in a teleconference. The teleconference=20 > will have to start sometime between 8am->8:30am PST to accommodate all > participants. We will try to arrange it for the end of next week.=20 > Given the large number of participants, it may be difficult to get a=20 > time that everyone can agree on. We'll aim to get at least one person=20 > from each institute/company. > > I've developed a tentative agenda below, but feel free to comment.=20 > Also this is intended to be an open group, so all are welcome. > > Agenda > =3D=3D=3D=3D=3D=3D > > 1. Introductions > 2. Agreement of general aims and purpose of standard 3. Review of=20 > existing standards=20 > http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in > NCBI ZTR format > = (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=3Dshow&f=3Dformats&m=3D= doc > &s > =3Dformats). > 4. Is a new standard necessary/requirements for new standard Possible=20 > discussion points > - human readable/something easily parsed by PERL ? > - combining sequence and quality values ? > - optionally referencing/utilizing existing ontologies for experiment > definition ? > - etc > 5. (If required) Framework for creating and approving the=20 > standard/discussion of IEEE role 6. Assignment of action items / next=20 > steps > > > Best Regards, > > > > Asim > > -------------------------------------------- > Asim Siddiqui, Ph.D. > Group Leader, Bioinformatics > Genome Sciences Centre > Suite 100 > > 570 West 7th Avenue > > Vancouver, BC > > Canada V5Z 4S6 > > > http://www.bcgsc.bc.ca Tel 604-707-5802 Fax > 604-877-6085 > > > > - Vladimir Alekseyev, NIH/NLM/NCBI Contractor From JSSadmin@bcgsc.ca Tue Jul 18 09:20:27 2006 Return-Path: X-Original-To: ssrformat@bcgsc.ca Delivered-To: ssrformat@bcgsc.ca Received: from xchange1.phage.bcgsc.ca (xchange1.bcgsc.bc.ca [10.9.208.35]) by mail.bcgsc.bc.ca (Postfix) with ESMTP id 555E3F00005A for ; Tue, 18 Jul 2006 09:20:27 -0700 (PDT) X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Date: Tue, 18 Jul 2006 09:20:27 -0700 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: short reads format Thread-Index: Acamk0xJw4YN2PSWSRycJvCTji2MigBB08WwALrGQmA= From: "JSSadmin" To: "Vladimir Alekseyev" , "Steven Jones" , , , "Gabor Marth" , "Aaron Quinlan" , "Michael Stromberg" , "Avak Kahvejian" , "Du, Lei" , "James Bonfield" , , "Rene Warren" , "Matthew Bainbridge" , , "Asim Siddiqui" , X-Mailman-Approved-At: Tue, 18 Jul 2006 10:30:42 -0700 Cc: Subject: [Ssrformat] RE: short reads format X-BeenThere: ssrformat@mail.bcgsc.ca X-Mailman-Version: 2.1.3 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 18 Jul 2006 16:20:29 -0000 Hi all, Please confirm the following details in your calendars: Short Reads format teleconference, Friday July 21, 8:00-9:30am PST. The dial in number is 604-707-4539 and the entry password is 085290. GSC Participants will meet in the 5th floor boardroom at Echelon. Please let me know if you have any further questions. Thanks, Shallom -----Original Message----- From: JSSadmin=20 Sent: Friday, July 14, 2006 4:17 PM To: 'Vladimir Alekseyev' Cc: Steven Jones; flicek@ebi.ac.uk; clive.Brown@solexa.com; Gabor Marth; Aaron Quinlan; Michael Stromberg; Avak Kahvejian; Du, Lei; James Bonfield; church@ncbi.nlm.nih.gov; Rene Warren; Matthew Bainbridge; ssrformat@bcgsc.ca; Asim Siddiqui; trace@ncbi.nlm.nih.gov Subject: RE: short reads format Hi all, With the exception of Vladmir, everyone who has replied is available on both dates. Therefore, I would like to confirm the teleconference date for Friday July 21st from 8:00-9:30am PST. If there is anyone who cannot make this time/date, please let me know. =20 For GSC participants, the 5th floor boardroom (Echelon) has been booked for your use. The room is reserved until 10am PST, just in case your meeting runs overtime. =20 For those of you calling in from other locations, I will be sending out an email on Monday with call-in details. Thanks, Shallom Shallom Ly and Charlotte Watts Administration to Dr. Steven Jones, Ms. Jacquie Schein and Dr. Asim Siddiqui Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency jssadmin@bcgsc.ca 604.707.5900 x 5413 (Shallom) 604.707.5900 x 5473 (Charlotte) -----Original Message----- From: Vladimir Alekseyev [mailto:aleksey@ncbi.nlm.nih.gov]=20 Sent: Thursday, July 13, 2006 8:45 AM To: JSSadmin Cc: Steven Jones; flicek@ebi.ac.uk; clive.Brown@solexa.com; Gabor Marth; Aaron Quinlan; Michael Stromberg; Avak Kahvejian; Du, Lei; James Bonfield; church@ncbi.nlm.nih.gov; Rene Warren; Matthew Bainbridge; ssrformat@bcgsc.ca; Asim Siddiqui; trace@ncbi.nlm.nih.gov Subject: RE: short reads format Hi, Unfortunately I will not be able to make on July 20th. I have another meeting at that time. Friday suites me better. In case you decide to teleconference on Thursday then Dimitry Volodin will be communicating with you. He will be our main developer for this project. Thanks, Vladimir Alekseyev On Wed, 12 Jul 2006, JSSadmin wrote: > Hi all, > > Please let me know which of the following timeslots is most convenient > for you: > > Thursday July 20th, 8:30-10:00am PST > Friday July 21st, 8:30-10:00am PST > > These are reserved as TBC in Asim's calendar. We could alternatively=20 > do a 8:00-9:30am PST timeslot, if that works better for everyone. > > Thanks, > Shallom > Shallom Ly and Charlotte Watts > Administration to Dr. Steven Jones, Ms. Jacquie Schein and Dr. Asim=20 > Siddiqui Canada's Michael Smith Genome Sciences Centre, BC Cancer=20 > Agency jssadmin@bcgsc.ca 604.707.5900 x 5413 (Shallom) 604.707.5900 x=20 > 5473 (Charlotte) > > ________________________________ > > From: Asim Siddiqui > Sent: Wednesday, July 12, 2006 2:07 PM > To: Steven Jones; flicek@ebi.ac.uk; clive.Brown@solexa.com; Gabor=20 > Marth; 'Aaron Quinlan'; 'Michael Stromberg'; Avak Kahvejian; Du, Lei;=20 > James Bonfield; aleksey@ncbi.nlm.nih.gov; church@ncbi.nlm.nih.gov;=20 > Rene Warren; Matthew Bainbridge; ssrformat@bcgsc.ca > Cc: JSSadmin > Subject: short reads format > > > Hi, > > You are receiving this e-mail because you have indicated an interest=20 > in developing a data format for short sequence reads. > > As noted in my previous e-mail, the standard will be open and=20 > machine/platform independent. > A mailing list (ssrformats@bcgsc.ca) has been created and you can sign > up for the list here http://www.bcgsc.ca/mailman/listinfo/ssrformat > > You will be contacted by JSSadmin@bcgsc.ca to determine your=20 > availability to participate in a teleconference. The teleconference=20 > will have to start sometime between 8am->8:30am PST to accommodate all > participants. We will try to arrange it for the end of next week.=20 > Given the large number of participants, it may be difficult to get a=20 > time that everyone can agree on. We'll aim to get at least one person=20 > from each institute/company. > > I've developed a tentative agenda below, but feel free to comment.=20 > Also this is intended to be an open group, so all are welcome. > > Agenda > =3D=3D=3D=3D=3D=3D > > 1. Introductions > 2. Agreement of general aims and purpose of standard 3. Review of=20 > existing standards=20 > http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in > NCBI ZTR format > = (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=3Dshow&f=3Dformats&m=3D= doc > &s > =3Dformats). > 4. Is a new standard necessary/requirements for new standard Possible=20 > discussion points > - human readable/something easily parsed by PERL ? > - combining sequence and quality values ? > - optionally referencing/utilizing existing ontologies for experiment > definition ? > - etc > 5. (If required) Framework for creating and approving the=20 > standard/discussion of IEEE role 6. Assignment of action items / next=20 > steps > > > Best Regards, > > > > Asim > > -------------------------------------------- > Asim Siddiqui, Ph.D. > Group Leader, Bioinformatics > Genome Sciences Centre > Suite 100 > > 570 West 7th Avenue > > Vancouver, BC > > Canada V5Z 4S6 > > > http://www.bcgsc.bc.ca Tel 604-707-5802 Fax > 604-877-6085 > > > > - Vladimir Alekseyev, NIH/NLM/NCBI Contractor From aleksey@ncbi.nlm.nih.gov Tue Jul 18 09:44:22 2006 Return-Path: X-Original-To: ssrformat@bcgsc.ca Delivered-To: ssrformat@bcgsc.ca Received: from gotland.bcgsc.bc.ca (gotland.bcgsc.bc.ca [10.9.208.74]) by mail.bcgsc.bc.ca (Postfix) with ESMTP id 21CB2F000058; Tue, 18 Jul 2006 09:44:22 -0700 (PDT) Received: from mailfwd.nih.gov (HELO nihrelayxway2.hub.nih.gov) ([128.231.90.107]) by gotland.bcgsc.bc.ca with ESMTP; 18 Jul 2006 09:44:21 -0700 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AQAAALKsvESKOwEBAgcECgcGHQ X-IronPort-AV: i="4.06,255,1149490800"; d="scan'208"; a="204542:sNHT27221730" Received: from hera.ncbi.nlm.nih.gov ([130.14.25.41]) by nihrelayxway2.hub.nih.gov with ESMTP; 18 Jul 2006 12:44:18 -0400 X-IronPortListener: NIH_Relay X-SBRS: None X-IronPort-AV: i="4.06,255,1149480000"; d="scan'208"; a="183210742:sNHT34452596" Date: Tue, 18 Jul 2006 12:44:17 -0400 (EDT) From: Vladimir Alekseyev To: JSSadmin In-Reply-To: Message-ID: References: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Mailman-Approved-At: Tue, 18 Jul 2006 10:30:42 -0700 Cc: Matthew Bainbridge , trace@ncbi.nlm.nih.gov, Rene Warren , church@ncbi.nlm.nih.gov, clive.Brown@solexa.com, ssrformat@bcgsc.ca, Avak Kahvejian , Aaron Quinlan , Steven Jones , "Du, Lei" , Michael Stromberg , flicek@ebi.ac.uk, Gabor Marth Subject: [Ssrformat] RE: short reads format X-BeenThere: ssrformat@mail.bcgsc.ca X-Mailman-Version: 2.1.3 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 18 Jul 2006 16:44:24 -0000 Here is a confirmation from NCBI. Just in case the phone number of our conference room is: 301-435-5171 Thanks, Vladimir On Tue, 18 Jul 2006, JSSadmin wrote: > Hi all, > > Please confirm the following details in your calendars: > > Short Reads format teleconference, Friday July 21, 8:00-9:30am PST. > The dial in number is 604-707-4539 and the entry password is 085290. > GSC Participants will meet in the 5th floor boardroom at Echelon. > > Please let me know if you have any further questions. > > Thanks, > Shallom > > > > > > -----Original Message----- > From: JSSadmin > Sent: Friday, July 14, 2006 4:17 PM > To: 'Vladimir Alekseyev' > Cc: Steven Jones; flicek@ebi.ac.uk; clive.Brown@solexa.com; Gabor Marth; > Aaron Quinlan; Michael Stromberg; Avak Kahvejian; Du, Lei; James > Bonfield; church@ncbi.nlm.nih.gov; Rene Warren; Matthew Bainbridge; > ssrformat@bcgsc.ca; Asim Siddiqui; trace@ncbi.nlm.nih.gov > Subject: RE: short reads format > > Hi all, > > With the exception of Vladmir, everyone who has replied is available on > both dates. Therefore, I would like to confirm the teleconference date > for Friday July 21st from 8:00-9:30am PST. > > If there is anyone who cannot make this time/date, please let me know. > > For GSC participants, the 5th floor boardroom (Echelon) has been booked > for your use. The room is reserved until 10am PST, just in case your > meeting runs overtime. > For those of you calling in from other locations, I will be sending out > an email on Monday with call-in details. > > Thanks, > Shallom > > Shallom Ly and Charlotte Watts > Administration to Dr. Steven Jones, Ms. Jacquie Schein and Dr. Asim > Siddiqui Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency > jssadmin@bcgsc.ca 604.707.5900 x 5413 (Shallom) 604.707.5900 x 5473 > (Charlotte) > > > > -----Original Message----- > From: Vladimir Alekseyev [mailto:aleksey@ncbi.nlm.nih.gov] > Sent: Thursday, July 13, 2006 8:45 AM > To: JSSadmin > Cc: Steven Jones; flicek@ebi.ac.uk; clive.Brown@solexa.com; Gabor Marth; > Aaron Quinlan; Michael Stromberg; Avak Kahvejian; Du, Lei; James > Bonfield; church@ncbi.nlm.nih.gov; Rene Warren; Matthew Bainbridge; > ssrformat@bcgsc.ca; Asim Siddiqui; trace@ncbi.nlm.nih.gov > Subject: RE: short reads format > > Hi, > > Unfortunately I will not be able to make on July 20th. I have another > meeting at that time. Friday suites me better. In case you decide to > teleconference on Thursday then Dimitry Volodin will be communicating > with you. He will be our main developer for this project. > > Thanks, > Vladimir Alekseyev > > On Wed, 12 Jul 2006, JSSadmin wrote: > > > Hi all, > > > > Please let me know which of the following timeslots is most convenient > > > for you: > > > > Thursday July 20th, 8:30-10:00am PST > > Friday July 21st, 8:30-10:00am PST > > > > These are reserved as TBC in Asim's calendar. We could alternatively > > do a 8:00-9:30am PST timeslot, if that works better for everyone. > > > > Thanks, > > Shallom > > Shallom Ly and Charlotte Watts > > Administration to Dr. Steven Jones, Ms. Jacquie Schein and Dr. Asim > > Siddiqui Canada's Michael Smith Genome Sciences Centre, BC Cancer > > Agency jssadmin@bcgsc.ca 604.707.5900 x 5413 (Shallom) 604.707.5900 x > > 5473 (Charlotte) > > > > ________________________________ > > > > From: Asim Siddiqui > > Sent: Wednesday, July 12, 2006 2:07 PM > > To: Steven Jones; flicek@ebi.ac.uk; clive.Brown@solexa.com; Gabor > > Marth; 'Aaron Quinlan'; 'Michael Stromberg'; Avak Kahvejian; Du, Lei; > > James Bonfield; aleksey@ncbi.nlm.nih.gov; church@ncbi.nlm.nih.gov; > > Rene Warren; Matthew Bainbridge; ssrformat@bcgsc.ca > > Cc: JSSadmin > > Subject: short reads format > > > > > > Hi, > > > > You are receiving this e-mail because you have indicated an interest > > in developing a data format for short sequence reads. > > > > As noted in my previous e-mail, the standard will be open and > > machine/platform independent. > > A mailing list (ssrformats@bcgsc.ca) has been created and you can sign > > > up for the list here http://www.bcgsc.ca/mailman/listinfo/ssrformat > > > > You will be contacted by JSSadmin@bcgsc.ca to determine your > > availability to participate in a teleconference. The teleconference > > will have to start sometime between 8am->8:30am PST to accommodate all > > > participants. We will try to arrange it for the end of next week. > > Given the large number of participants, it may be difficult to get a > > time that everyone can agree on. We'll aim to get at least one person > > from each institute/company. > > > > I've developed a tentative agenda below, but feel free to comment. > > Also this is intended to be an open group, so all are welcome. > > > > Agenda > > ====== > > > > 1. Introductions > > 2. Agreement of general aims and purpose of standard 3. Review of > > existing standards > > http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in > > NCBI ZTR format > > (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc > > &s > > =formats). > > 4. Is a new standard necessary/requirements for new standard Possible > > discussion points > > - human readable/something easily parsed by PERL ? > > - combining sequence and quality values ? > > - optionally referencing/utilizing existing ontologies for experiment > > > definition ? > > - etc > > 5. (If required) Framework for creating and approving the > > standard/discussion of IEEE role 6. Assignment of action items / next > > steps > > > > > > Best Regards, > > > > > > > > Asim > > > > -------------------------------------------- > > Asim Siddiqui, Ph.D. > > Group Leader, Bioinformatics > > Genome Sciences Centre > > Suite 100 > > > > 570 West 7th Avenue > > > > Vancouver, BC > > > > Canada V5Z 4S6 > > > > > > http://www.bcgsc.bc.ca Tel 604-707-5802 Fax > > > 604-877-6085 > > > > > > > > > > - > Vladimir Alekseyev, > NIH/NLM/NCBI Contractor > - Vladimir Alekseyev, NIH/NLM/NCBI Contractor From jkb@sanger.ac.uk Fri Jul 21 03:22:59 2006 Return-Path: X-Original-To: ssrformat@bcgsc.ca Delivered-To: ssrformat@bcgsc.ca Received: from gotland.bcgsc.bc.ca (gotland.bcgsc.bc.ca [10.9.208.74]) by mail.bcgsc.bc.ca (Postfix) with ESMTP id BA381F00005E; Fri, 21 Jul 2006 03:22:58 -0700 (PDT) Received: from smtp.sanger.ac.uk ([193.62.203.215]) by gotland.bcgsc.bc.ca with ESMTP; 21 Jul 2006 03:22:57 -0700 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AQAAAMtFwESKPgEBAQgOKg X-IronPort-AV: i="4.07,166,1151910000"; d="scan'208"; a="216127:sNHT66437520" Received: from deskpro16133.dynamic.sanger.ac.uk ([172.19.32.236]) by intmail1b.internal.sanger.ac.uk with esmtp (Exim 4.41) id 1G3s9j-00041z-Fk; Fri, 21 Jul 2006 11:22:51 +0100 Received: by deskpro16133.dynamic.sanger.ac.uk (Postfix, from userid 205) id F267A32C0E9; Fri, 21 Jul 2006 11:22:49 +0100 (BST) Date: Fri, 21 Jul 2006 11:22:49 +0100 From: James Bonfield To: JSSadmin Message-ID: <20060721102249.GL17306@cbi1.sanger.ac.uk> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: User-Agent: Mutt/1.5.9i X-Mailman-Approved-At: Fri, 21 Jul 2006 09:01:50 -0700 Cc: Matthew Bainbridge , Vladimir Alekseyev , trace@ncbi.nlm.nih.gov, Rene Warren , church@ncbi.nlm.nih.gov, clive.Brown@solexa.com, ssrformat@bcgsc.ca, Avak Kahvejian , Aaron Quinlan , Steven Jones , "Du, Lei" , Michael Stromberg , flicek@ebi.ac.uk, Gabor Marth Subject: [Ssrformat] Re: short reads format X-BeenThere: ssrformat@mail.bcgsc.ca X-Mailman-Version: 2.1.3 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 21 Jul 2006 10:23:02 -0000 On Tue, Jul 18, 2006 at 09:20:27AM -0700, JSSadmin wrote: > Short Reads format teleconference, Friday July 21, 8:00-9:30am PST. > The dial in number is 604-707-4539 and the entry password is 085290. > GSC Participants will meet in the 5th floor boardroom at Echelon. Sorry for the late reply. I assume by 8am PST you mean PST with daylight savings (ie PDT?), aka UTC-7. I should now be able to attend this and hopefully Steve Leonard who maintains the Ensembl trace server will be attending too. James -- James Bonfield (jkb@sanger.ac.uk) A Staden Package developer: https://sourceforge.net/projects/staden/ From asims@bcgsc.ca Fri Jul 21 07:55:31 2006 Return-Path: X-Original-To: ssrformat@bcgsc.ca Delivered-To: ssrformat@bcgsc.ca Received: from xchange1.phage.bcgsc.ca (xchange1.bcgsc.bc.ca [10.9.208.35]) by mail.bcgsc.bc.ca (Postfix) with ESMTP id 2115FF000064 for ; Fri, 21 Jul 2006 07:55:31 -0700 (PDT) X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Date: Fri, 21 Jul 2006 07:55:29 -0700 Message-ID: <86C6E520C12E52429ACBCB01546DF4D3E95ECA@xchange1.phage.bcgsc.ca> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: short reads format Thread-Index: Acasr6ocK7RIJs/DQ8eewkaDrKaBEAAJgCJA From: "Asim Siddiqui" To: "James Bonfield" , "JSSadmin" X-Mailman-Approved-At: Fri, 21 Jul 2006 09:01:50 -0700 Cc: Matthew Bainbridge , Vladimir Alekseyev , trace@ncbi.nlm.nih.gov, Rene Warren , church@ncbi.nlm.nih.gov, clive.Brown@solexa.com, ssrformat@bcgsc.ca, Avak Kahvejian , Aaron Quinlan , Steven Jones , "Du, Lei" , Michael Stromberg , flicek@ebi.ac.uk, Gabor Marth Subject: [Ssrformat] RE: short reads format X-BeenThere: ssrformat@mail.bcgsc.ca X-Mailman-Version: 2.1.3 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 21 Jul 2006 14:55:33 -0000 Yes, that's correct. Talk to you in a couple of minutes.=20 -----Original Message----- From: James Bonfield [mailto:jkb@sanger.ac.uk]=20 Sent: Friday, July 21, 2006 3:23 AM To: JSSadmin Cc: Vladimir Alekseyev; Steven Jones; flicek@ebi.ac.uk; clive.Brown@solexa.com; Gabor Marth; Aaron Quinlan; Michael Stromberg; Avak Kahvejian; Du, Lei; church@ncbi.nlm.nih.gov; Rene Warren; Matthew Bainbridge; ssrformat@bcgsc.ca; Asim Siddiqui; trace@ncbi.nlm.nih.gov Subject: Re: short reads format On Tue, Jul 18, 2006 at 09:20:27AM -0700, JSSadmin wrote: > Short Reads format teleconference, Friday July 21, 8:00-9:30am PST. > The dial in number is 604-707-4539 and the entry password is 085290. > GSC Participants will meet in the 5th floor boardroom at Echelon. Sorry for the late reply. I assume by 8am PST you mean PST with daylight savings (ie PDT?), aka UTC-7. I should now be able to attend this and hopefully Steve Leonard who maintains the Ensembl trace server will be attending too. James -- James Bonfield (jkb@sanger.ac.uk) A Staden Package developer: https://sourceforge.net/projects/staden/ From aleksey@ncbi.nlm.nih.gov Fri Jul 21 09:37:11 2006 Return-Path: X-Original-To: ssrformat@bcgsc.ca Delivered-To: ssrformat@bcgsc.ca Received: from gotland.bcgsc.bc.ca (gotland.bcgsc.bc.ca [10.9.208.74]) by mail.bcgsc.bc.ca (Postfix) with ESMTP id C342BF00005A; Fri, 21 Jul 2006 09:37:10 -0700 (PDT) Received: from nihcessmtp.hub.nih.gov ([128.231.90.115]) by gotland.bcgsc.bc.ca with ESMTP; 21 Jul 2006 09:37:10 -0700 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AQAAAOGewESKPgEBAQEHBAoHBh0 X-IronPort-AV: i="4.07,169,1151910000"; d="scan'208"; a="217119:sNHT28347380" Received: from NIHCESMLBX8.nih.gov ([156.40.71.208]) by NIHCESSMTP.hub.nih.gov with Microsoft SMTPSVC(6.0.3790.1830); Fri, 21 Jul 2006 12:37:08 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Date: Fri, 21 Jul 2006 12:37:06 -0400 Message-ID: <7F40ACD22B0A23448C4E8755E5875FE704FD348A@NIHCESMLBX8.nih.gov> In-Reply-To: <86C6E520C12E52429ACBCB01546DF4D3E95ECA@xchange1.phage.bcgsc.ca> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: short reads format Thread-Index: Acasr6ocK7RIJs/DQ8eewkaDrKaBEAAJgCJAAALoeVA= From: "Alekseyev, Vladimir (NIH/NLM/NCBI) [C]" To: "Asim Siddiqui" , "James Bonfield" , "JSSadmin" X-OriginalArrivalTime: 21 Jul 2006 16:37:08.0528 (UTC) FILETIME=[E885E300:01C6ACE3] X-Mailman-Approved-At: Mon, 24 Jul 2006 10:28:23 -0700 Cc: Matthew Bainbridge , NLM/NCBI List trace , Rene Warren , "Church, Deanna $NIH/NLM/NCBI$ \[E\]" , clive.Brown@solexa.com, ssrformat@bcgsc.ca, Avak Kahvejian , Aaron Quinlan , Steven Jones , "Du, Lei" , Michael Stromberg , flicek@ebi.ac.uk, Gabor Marth Subject: [Ssrformat] RE: short reads format X-BeenThere: ssrformat@mail.bcgsc.ca X-Mailman-Version: 2.1.3 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 21 Jul 2006 16:37:13 -0000 As a follow up of the conference call here is the NCBI Trace Assembly submission format: The list of current assemblies can be viewed here as a tree: Or as a list: To download an assembly from ftp click on the 'diskette' icon. To view a particular assembly click on the Assembly ID: We have a few minor problems with the assembly viewer 'though. The problems hopefully will be fixed with the new version of it which we are going to install into the production next week. If you encounter a problem, try to reload the viewer, usually it works fine after that. Thanks, Vladimir >-----Original Message----- >From: Asim Siddiqui [mailto:asims@bcgsc.ca]=20 >Sent: Friday, July 21, 2006 10:55 AM >To: James Bonfield; JSSadmin >Cc: Alekseyev, Vladimir (NIH/NLM/NCBI) [C]; Steven Jones;=20 >flicek@ebi.ac.uk; clive.Brown@solexa.com; Gabor Marth; Aaron=20 >Quinlan; Michael Stromberg; Avak Kahvejian; Du, Lei; Church,=20 >Deanna (NIH/NLM/NCBI) [E]; Rene Warren; Matthew Bainbridge;=20 >ssrformat@bcgsc.ca; NLM/NCBI List trace >Subject: RE: short reads format > > >Yes, that's correct. Talk to you in a couple of minutes.=20 > >-----Original Message----- >From: James Bonfield [mailto:jkb@sanger.ac.uk] >Sent: Friday, July 21, 2006 3:23 AM >To: JSSadmin >Cc: Vladimir Alekseyev; Steven Jones; flicek@ebi.ac.uk;=20 >clive.Brown@solexa.com; Gabor Marth; Aaron Quinlan; Michael=20 >Stromberg; Avak Kahvejian; Du, Lei; church@ncbi.nlm.nih.gov;=20 >Rene Warren; Matthew Bainbridge; ssrformat@bcgsc.ca; Asim=20 >Siddiqui; trace@ncbi.nlm.nih.gov >Subject: Re: short reads format > >On Tue, Jul 18, 2006 at 09:20:27AM -0700, JSSadmin wrote: >> Short Reads format teleconference, Friday July 21, 8:00-9:30am PST. >> The dial in number is 604-707-4539 and the entry password is 085290. >> GSC Participants will meet in the 5th floor boardroom at Echelon. > >Sorry for the late reply. I assume by 8am PST you mean PST=20 >with daylight savings (ie PDT?), aka UTC-7. > >I should now be able to attend this and hopefully Steve=20 >Leonard who maintains the Ensembl trace server will be attending too. > >James > >-- >James Bonfield (jkb@sanger.ac.uk) >A Staden Package developer: https://sourceforge.net/projects/staden/ > From asims@bcgsc.ca Fri Jul 21 09:51:09 2006 Return-Path: X-Original-To: ssrformat@bcgsc.ca Delivered-To: ssrformat@bcgsc.ca Received: from xchange1.phage.bcgsc.ca (xchange1.bcgsc.bc.ca [10.9.208.35]) by mail.bcgsc.bc.ca (Postfix) with ESMTP id 93268F000060 for ; Fri, 21 Jul 2006 09:51:09 -0700 (PDT) X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C6ACE5.DDCF872E" Date: Fri, 21 Jul 2006 09:51:08 -0700 Message-ID: <86C6E520C12E52429ACBCB01546DF4D3E95ECE@xchange1.phage.bcgsc.ca> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Minutes from short sequence reads format meeting Thread-Index: Acas5d1UEci1iyB7SweyT1Oy7SFQJw== From: "Asim Siddiqui" To: "Vladimir Alekseyev" , "Steven Jones" , , , "Gabor Marth" , "Aaron Quinlan" , "Michael Stromberg" , "Du, Lei" , "James Bonfield" , , "Rene Warren" , "Matthew Bainbridge" , , "Asim Siddiqui" , X-Mailman-Approved-At: Mon, 24 Jul 2006 10:28:23 -0700 Cc: Subject: [Ssrformat] Minutes from short sequence reads format meeting X-BeenThere: ssrformat@mail.bcgsc.ca X-Mailman-Version: 2.1.3 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 21 Jul 2006 16:51:12 -0000 This is a multi-part message in MIME format. ------_=_NextPart_001_01C6ACE5.DDCF872E Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable I didn't get everyone's name. If your name is spelled incorrectly or you notice that other names are missing, please let me know. =20 Please send any corrections to the minutes by the end of next week. =20 Next meeting will take place in ~1 month =20 Meeting: Short sequence reads format Date/Time: 21st July, 8am PDT =20 Present: Vladimir Alekseyev (NCBI), Paul Flicek (EBI), Clive Brown (Solexa), Tony Cox (Solexa), Klaus M (Solexa), Collin Goddard (Solexa), Gabor Marth (Boston College), Aaron Quinlan (Boston College), Michael Stromberg (Boston College), Lei Du (454), James Bonfield (Sanger), Steve Lenard (Sanger) Deanna Church (NCBI), Rene Warren (BC GSC), Ed Thayer (Helicos), Asim Siddiqui (BC GSC) =20 Regrets received: Steven Jones (BC GSC) =20 Actions: Action: Asim to invite David Jaffe to the group. Action: James to send link to his source code for ZTR file creation. Action: Clive/Solexa to try to submit data to NCBI Action: Ed/Helicos to try to submit data to NCBI Action: Gabor to send CAF assembly format link Action: Deanna to send NCBI assembly format link=20 Action: Lei to invite James Knight (454). =20 Decisions: Decision: Images will not be stored. Decision: Generic trace format possible, but the interpretation of the information stored will be different for different technologies. Decision: ZRT format will be used for trace files. Decision: Once individual formats are created, we will try to remove redundancies and create a single format. =20 1. Introductions =20 Introductions made.=20 Asim had not had time to contact David Jaffe, but Clive had spoken with him Action: Asim to invite David Jaffe to the group. =20 2. Discussion of formats Trace format and assembly format a) Trace format Trace format exists for 454. The error model for data from 454 is quite different from Solexa. 454 primary errors are insertions/deletions. Solexa primary error are substitutions. Clive suggested that most other sequencers would likely have the Solexa error model. =20 James/Clive: It was suggested that the error model type could be captured in a file header. The format of the bulk of the file would facilitate easy processing by "dumb" parsers. A parser that needed to display the data would need to understand the error model to correctly display it. =20 James?: Finishers will want to be able to determine how the base was called and will want to see trace level information. Need random level access into files. =20 Gabor/Clive: Images are "Level 1" information and will not be stored. =20 Decision: Images will not be stored. =20 James: 3 types of information to store for all sequencers: 1) base calls, 2) competence values, 3) binary values. Data stored in these fields by different sequencing technologies would require different interpretations. =20 Decision: Generic trace format possible, but the interpretation of the information stored will be different for different technologies. =20 James: ZTR format can presently support these requirements. =20 Dmitry: In response to Asim's question (who has only performed bit level file manipulations in C/C++!), yes, PERL does support bit level access, so the data would be generally accessible. Also raised the question of using XML. =20 Someone: XML would inflate file size =20 Asim: Could use XML for the header information and ZTR for the rest =20 Deanna: In response to question from Gabor on experiment conditions, trace archive has extensive XML format for such data. =20 Decision: ZRT format will be used for trace files. =20 Action: James to send link to his source code for ZTR file creation. =20 Action: Clive/Solexa to try to submit data to NCBI Action: Ed/Helicos to try to submit data to NCBI =20 Decision: Once individual formats are created, we will try to remove redundancies and create a single format. =20 b) Assembly format =20 General discussion on some of the issues faced here. =20 Action: Gabor to send CAF assembly format link Action: Deanna to send NCBI assembly format link=20 =20 3) Next meeting in 1 month =20 Action: Lei to invite James Knight (454). =20 =20 =20 =20 =20 =20 ------_=_NextPart_001_01C6ACE5.DDCF872E Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

I = didn't get=20 everyone's name. If your name is spelled incorrectly or you notice that = other=20 names are missing, please let me know.

Please = send any=20 corrections to the minutes by the end of next week.

Next = meeting will=20 take place in ~1 month

Meeting: Short=20 sequence reads format

Date/Time: 21st=20 July, 8am PDT

Present: Vladimir=20 Alekseyev (NCBI), Paul Flicek (EBI), Clive Brown (Solexa), Tony Cox = (Solexa),=20 Klaus M (Solexa), Collin Goddard (Solexa), Gabor Marth (Boston College), = Aaron=20 Quinlan (Boston College), Michael Stromberg (Boston College), Lei Du = (454),=20 James Bonfield (Sanger), Steve Lenard (Sanger) Deanna Church (NCBI), = Rene Warren=20 (BC GSC), Ed Thayer (Helicos), Asim Siddiqui (BC = GSC)

Regrets received:=20 Steven Jones (BC GSC)

Actions:

Action: Asim to invite David Jaffe to the=20 group.

Action: James to=20 send link to his source code for ZTR file creation.

Action: Clive/Solexa=20 to try to submit data to NCBI

Action: Ed/Helicos=20 to try to submit data to = NCBI

Action: Gabor to=20 send CAF assembly format link

Action: Deanna to=20 send NCBI assembly format link

Action: Lei to invite James Knight=20 (454).

Decisions:

Decision: Images=20 will not be stored.

Decision: Generic=20 trace format possible, but the interpretation of = the information=20 stored will be different for different technologies.

Decision: ZRT format=20 will be used for trace files.

Decision: Once=20 individual formats are created, we will try to remove redundancies and = create a=20 single=20 format.

1.=20 Introductions

Introductions made.=20

Asim = had not had=20 time to contact David Jaffe, but Clive had spoken with = him

Action: Asim to=20 invite David Jaffe to the group.

2. = Discussion of=20 formats

Trace = format and=20 assembly format

a) = Trace=20 format

Trace = format exists=20 for 454.

The = error model for=20 data from 454 is quite different from Solexa. 454 primary errors are=20 insertions/deletions. Solexa primary error are=20 substitutions.

Clive = suggested that=20 most other sequencers would likely have the Solexa error=20 model.

James/Clive: It was=20 suggested that the error model type could be captured in a file header. = The=20 format of the bulk of the file would facilitate easy = processing=20 by "dumb" parsers.

A = parser that needed=20 to display the data would need to understand the error model to = correctly=20 display it.

James?: Finishers=20 will want to be able to determine how the base was called and will want = to see=20 trace level information. Need random level access into=20 files.

Gabor/Clive: Images=20 are "Level 1" information and will not be stored.

Decision: Images=20 will not be stored.

James: = 3 types of=20 information to store for all sequencers: 1) base calls, 2) competence = values, 3)=20 binary values.

Data = stored in these=20 fields by different sequencing technologies would require different = interpretations.

Decision: Generic=20 trace format possible, but the interpretation of = the information=20 stored will be different for different technologies.

James: = ZTR format=20 can presently support these requirements.

Dmitry: In response=20 to Asim's question (who has only performed bit level file=20 manipulations in C/C++!), yes, PERL does support bit level access, so = the data=20 would be generally accessible.

Also = raised the=20 question of using XML.

Someone: XML would=20 inflate file size

Asim: = Could use XML=20 for the header information and ZTR for the rest

Deanna: In response=20 to question from Gabor on experiment conditions, trace archive has = extensive XML=20 format for such data.

Decision: ZRT format=20 will be used for trace files.

Action: James to=20 send link to his source code for ZTR file creation.

Action: Clive/Solexa=20 to try to submit data to NCBI

Action: Ed/Helicos=20 to try to submit data to NCBI

Decision: Once=20 individual formats are created, we will try to remove redundancies and = create a=20 single format.

b) = Assembly=20 format

General discussion=20 on some of the issues faced here.

Action: Gabor to=20 send CAF assembly format link

Action: Deanna to=20 send NCBI assembly format link

3) = Next meeting in 1=20 month

Action: Lei to=20 invite James Knight (454).

------_=_NextPart_001_01C6ACE5.DDCF872E-- From jkb@sanger.ac.uk Mon Jul 24 04:22:24 2006 Return-Path: X-Original-To: ssrformat@bcgsc.ca Delivered-To: ssrformat@bcgsc.ca Received: from gotland.bcgsc.bc.ca (gotland.bcgsc.bc.ca [10.9.208.74]) by mail.bcgsc.bc.ca (Postfix) with ESMTP id 87B9AF0000BF; Mon, 24 Jul 2006 04:22:23 -0700 (PDT) Received: from smtp.sanger.ac.uk ([193.62.203.215]) by gotland.bcgsc.bc.ca with ESMTP; 24 Jul 2006 04:22:22 -0700 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AQAAAAtJxESKRgEBAgcOKg X-IronPort-AV: i="4.07,174,1151910000"; d="scan'208"; a="226773:sNHT48288600" Received: from deskpro16133.dynamic.sanger.ac.uk ([172.19.32.236]) by intmail1b.internal.sanger.ac.uk with esmtp (Exim 4.41) id 1G4yVu-0007qL-Hu; Mon, 24 Jul 2006 12:22:18 +0100 Received: by deskpro16133.dynamic.sanger.ac.uk (Postfix, from userid 205) id 3E23132C0EB; Mon, 24 Jul 2006 12:22:08 +0100 (BST) Date: Mon, 24 Jul 2006 12:22:08 +0100 From: James Bonfield To: Asim Siddiqui Message-ID: <20060724112207.GT17306@cbi1.sanger.ac.uk> References: <86C6E520C12E52429ACBCB01546DF4D3E95ECE@xchange1.phage.bcgsc.ca> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="vtzGhvizbBRQ85DL" Content-Disposition: inline In-Reply-To: <86C6E520C12E52429ACBCB01546DF4D3E95ECE@xchange1.phage.bcgsc.ca> User-Agent: Mutt/1.5.9i X-Mailman-Approved-At: Mon, 24 Jul 2006 10:28:23 -0700 Cc: Matthew Bainbridge , Vladimir Alekseyev , trace@ncbi.nlm.nih.gov, Rene Warren , church@ncbi.nlm.nih.gov, Steven Leonard , clive.Brown@solexa.com, ssrformat@bcgsc.ca, Aaron Quinlan , Steven Jones , "Du, Lei" , Michael Stromberg , flicek@ebi.ac.uk, Gabor Marth Subject: [Ssrformat] More thoughts of ssr file formats X-BeenThere: ssrformat@mail.bcgsc.ca X-Mailman-Version: 2.1.3 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 24 Jul 2006 11:22:26 -0000 --vtzGhvizbBRQ85DL Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Hello all, At our meeting we discussed file formats and agreed that ZTR has something to offer. However with hindsight I think we glossed over the "archive" aspect of it all. ZTR is a single file format, much like gif and jpg are for images. My own use of ztr archives is a different issue - it works well for me, but maybe isn't entirely optimal for our group requirements. So I've tried to formalise the points a bit. As far as I can see we need to satisfy multiple parties here. - Submission formats to NCBI / Ensembl trace archives. Needs a streamable format for ease of loading. - Output formats from machine manufacturers. Needs to be easy to write and public. - Distribution formats for callaboraters working on projects. Size is a key issue here too as it directly translates to network bandwidth for transfering files. - Random access formats to provide rapid viewing of specific traces within finishing programs (gap4, consed, etc). I'm attaching a couple of documents explaining my views on a potential new container and details of how my existing "hash-file" system works to provide indices for arbitrary formats (tested on 454's SFF, "solid" archives of solexa data in ZTR format and tar files). All comments welcomed! I'll try my best to incorporate whatever we decide on in the C io_lib library for reading and writing trace files. This code is free and unencumbered: https://sourceforge.net/project/showfiles.php?group_id=100316&package_id=108243 For the ZTR format I have some specs at: http://staden.sourceforge.net/ztr.html There's also a paper on the format: Bonfield, James K. and Staden, Rodger. ZTR: a new format for DNA sequence trace data. Bioinformatics 18, 3-10, (2002). http://bioinformatics.oxfordjournals.org/cgi/reprint/18/1/3.pdf James -- James Bonfield (jkb@sanger.ac.uk) A Staden Package developer: https://sourceforge.net/projects/staden/ --vtzGhvizbBRQ85DL Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename=FORMATS Containers vs files =================== I think there is a clear and distinct separation between file formats and container formats. Tar and zip are two examples of containers while GIF and JPG are example image formats. The two serve different purposes and yet we're perfectly happy with the notion of being given a tar file containing jpg images. We may need to consider the same concepts for trace files. We want to have a file format for housing traces and a container to reduce the number of files on disk. At our meeting we didn't really discuss containers much. We can't simply use tar as it's crippling in the default block size. Storing lots of separate traces of maybe 500 bytes each in an archive that uses 512 bytes header and a subsequent block size of 512 bytes for file contents is very inefficient. Cpio and ZIP are better, but suffer other problems. Currently we have an example container already in use for short reads: SFF. It has some useful features which are worthy of noting. 1) It has a header to indicate a magic number and version 2) The container header also has elements common to every file within it (this is somewhat specialist and breaks the separation from file format to container format). I call this a file "prefix" below. 3) Each file contained within it has a name and size associated with it, making streaming through the archive simple. 4) It optionally has an index allowing for random access within it. 5) It is 64-bit clean; handling archives > 2Gb in size. Conversely it's too specific to 454. The header to be added to every archive entry is specifically hard coded to store the flow order, and the global archive header also has specifics for 454. Additionally the file header has things like number of bases and clip points in it. While not unique to 454, I think maybe this really should be in the read data section (as not all machines need to store number of bases - eg it's fixed archive-wide in Solexa). My own ZTR archives are a bit cruder. Currently I just threw together all the ztr files (literally equivalent to "cat *.ztr") while at the same time tracking the start and size of each component so they could be added to a hash table based index at the end of the file. This makes random access quick and easy, but breaks point 3) above as streaming is awkward (you'd need to load the index and re-sort first). In essence all the "container format" part of this is within the index itself. So in short the current ZTR archive situation is workable, but in my opinion not optimal. My hash table index also contained the notion of a file header or file footer. Each entry in the index consists of a name, position, size and an indicator of which (if any) header and footer to use. Put simply the file extracted from the archive is then header + file + footer concatenated together. This allowed emulation of 454 SFF archives and indeed the hash table can be used as an alternate indexing technique so that the general purpose hash-file tools can extract entries out of an SFF archive without any knowledge of the data type is dealing with. Similarly the same hash-file tools can be used to index and extract out of tar, cpio or other archive formats. However with hindsight I see problems with this too. In the context of a ZTR archive the index is mandatory as it's the only place reading names are held, therefore streaming cannot be achieved and it's hard to merge archives. (The same is true for merging SFF archives too though.) One solution to this is to add new ZTR chunk types: NAME The sample name EOF_ Chunk header only, with data length set to zero. Marks the end of this ZTR file. This would allow streaming of sorts by changing the ztr code so that it stops reading once it sees an EOF_ chunk, but practically it may require some restructuring of existing decoders to manage this (which slurp the entire file into memory and then decode it once there). A more workable solution is to intersperse the ZTR files with a small header indicating name and size, effectively creating our own simple container format. This then means that the name is duplicated in both the archive and the archive index, but streaming and decoding is trivial. It doesn't easily overcome the common prefix issue though. It may seem that the notion of a common prefix tacked on to the front of every trace implies that the prefix data should really be stored in the associated traceinfo.xml file. However for 454 data the common element is simply the flow order. This is required for both base calling and display of the trace data so I feel it is appropriate for it to be part of the binary trace file itself. Archive contatenation is a trickier one too. We may have to accept it's not easily doable without special tools, but if we allow for a duplicate header half way through the file to be ignored then we can simply "cat *.archive > new_arc" to merge multiple archives together. Questions: Is there any need to be able to easily merge archives? Do we want to construct a completely new "container" format, capable of handling any internal data format in an abstract manner? Possible container format ========================= Given that the existing general purpose containers (eg zip) don't seem to handle things like file headers well and SFF is specialised for 454, I propose that we come up with a new general format. It allows for streaming, concatenation and indexing for random-access. Basic Structure --------------- Block Block Block... Where each Block is one of: Container header block (magic numbers, versions, file prefixes) File blocks (names, data) - many copies of these Index block Typically a file will contain 1 container header followed by N file blocks and optionally 1 index block. If we've contatenated multiple archives together then it'll go back to a 2nd container header, another M file blocks, etc. Each block has bits 0-7 as a block type and then bits 32-63 as the block size. Bits 8-31 have meaning specific to each block type and may simply be nulls. The gap was left simply to keep the size 32-bit word-aligned for each of decoding. This means that a streaming process can decode the header block and any file blocks and skip index blocks (or any future blocks we may wish to insert) without understanding their format. Any "common prefix" blocks in a container header are only valid until the next container header is found. Container header ---------------- uint8_t Block type ('C') uint24_t Magic number (actually uint32_t with the block type being part of the magic number) uint32_t Block size (includes file prefixes below) char[4] Version uint64_t Index offset (0 if not present) uint32_t Index length uint32_t Number of file prefixes (NP) uint32_t prefix size \ (NP copies) char *prefix_contents / The first 8 bits of magic number also serve as a block type, here indicating it's the container header. The magic number shouldn't be plain text incase arbitrary text files are mistaken as containers according to their magic number. Use "Cnt^Z"? Has the benefit of causing EOF for any non-binary access modes attempted on windows, rather than giving broken data due to cr/nl bugs instead. Need to also check what extensions are appropriate and already reserved. We count prefix numbers starting from 1 so that 0 can be used to imply none needed. This makes quickly seeking to find the data for prefix 'N' awkward and we could maybe solve this by storing all sizes and then all contents, but in practice I doubt it'll make any difference. Comments? In streaming mode we'll likely just load the entire lot up and cache it. In random access mode we can also load it all in a single read and decode in memory. Alternatively we can just have a "sub-block" instead of header or footer being separate. And then in the file header we can indicate the order in which objects appear. Eg a data structure indicating "block 1 + file data + block 2". I suspect that's overkill though. File header ----------- uint8_t block_type ('F') uint8_t prefix_number uint16_t name_length uint32_t block_size This is then followed by the name and data itself. The length of the file is implicitly the remainder of block_size. Ie: char name[name_length] char data[block_size - 8 - name_length] This gives an overhead of 8 + strlen(name) per file. For solexa and 454 data this is likely to be only 1-2%. Limitations: Names are limited to 65535 bytes (not a problem in my opinion) and file contents are limited to 4Gb. (Plenty for our purposes, but maybe not for a general purpose container.) Index ----- uint8_t block_type ('I') uint8_t padding[3] uint32_t index_size uint64_t bytes since 'start of file' (or last index) ... HashFile index ... I need to think more on how to adapt my existing hashed index to this. I'm attaching docs on the existing hash-file format which is already in use by Gap4. If we concatenate multiple indexed archives together then the index needs to hold a pointer to the previous index (or specifically it's own offset since the start of the file prior to concatenation) so that random extraction allows for skipping back through indices. Alternatively an optimiser could restructure the file to collapse the multiple copies and produce a single common header and one single index. This is effectively a dedicated archive "cat" tool to do the merging of archives for us. It may be a more workable solution compared to the hoops we need to jump through to make archives trivially concatenateable by unix "cat". --vtzGhvizbBRQ85DL Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename=Hash_File_Format A Hash File is an on-disk copy of a Hash Table keyed by filenames and with data containing a file size and position within an archive. It's designed to be a general purpose indexing tool for most archive formats or for "solid" (concatenated) file archives. Basic operations need to be performed on hash files and there are tools to do this: Listing the contents hash_list [-l] Extraction hash_extract Concatenation hash_cat The Hash File format is: Header, archive file name, file headers/footers, hash buckets, hash linked list items, footer. In more detail: Header: ".hsh" (magic numebr) x4 (1-bytes of version code, eg "1.00") x1 (HASH_FUNC_? function used) x1 (number of file headers: FH. These count from 1 to FH inclusive) x1 (number of file footers: FF. These count from 1 to FF inclusive) x1 (reserved - zero for now) x4 (4-bytes big-endian; number of hash buckets) x8 (offset to add to item positions. eg size of this index) x4 (total size of hashfile, includingf header, ..., index, footer) Archive name: x1 (length 'L', zero => no name) xL (archive filename) File headers (FH copies of): x8 (position) x4 (size) File footers (FH copies of): x8 (position) x4 (size) Buckets (multiples of) x4 (4-byte offset of linked list pos, rel. to the start of the hdr) Items (per bucket chain, not written if Bucket[?]==0) x1 (key length 'K', zero => end of chain) xK (key) x0.5 (File header to use. zero => none) top 4 bits x0.5 (File footer to use. zero => none) bottom 4 bits x8 (position) x4 (size) Index footer: ".hsh" (magic number) x8 (offset to Hash Header. >=0 = absolute, -ve = relative to end) The HashFile index may either be a separate file to the archive, in which case the "Archive name" section references the archive itself, or part of the archive itself in which case archive name is zero length. Additionally if the archive name length is non-zero but the first byte of the archive filename is zero then it is also considered to be part of the same archive. This allows for an index previously generated as a separate file to simply be appended to the archive with a minimal of binary editing (ie zeroing 1 byte). The HashFile index may also be at the start (preferred and searched for first) or the end of the file. This is the rationale behind having an index footer. It allows us to simply append a hash of a tar file to the end of the tar file itself and it'll work just fine without breaking the format of the tar file. (Tar files end with a blank block, so additional data is not read by tar.) Appending the hashfile requires an extra 2 seeks and 1 read (if opening from scratch) to fetch a file compared to prepending the hashfile. If the hash file was originally stored as a separate file from the archive but is now being merged then zero the first byte of the archive filename and either prepend or append as desired. If you prepend the hash file then note that all the absolute offsets in the Item structures will now be incorrect. A correction factor may be applied, of the size of the HashFile itself, and this is the purpose of the offset field in the header. --vtzGhvizbBRQ85DL-- From jkb@sanger.ac.uk Mon Jul 24 04:33:44 2006 Return-Path: X-Original-To: ssrformat@bcgsc.ca Delivered-To: ssrformat@bcgsc.ca Received: from gotland.bcgsc.bc.ca (gotland.bcgsc.bc.ca [10.9.208.74]) by mail.bcgsc.bc.ca (Postfix) with ESMTP id 86F19F0000BF; Mon, 24 Jul 2006 04:33:43 -0700 (PDT) Received: from smtp.sanger.ac.uk ([193.62.203.215]) by gotland.bcgsc.bc.ca with ESMTP; 24 Jul 2006 04:33:42 -0700 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AQAAAJ9LxESKRgEBAgcOKg X-IronPort-AV: i="4.07,175,1151910000"; d="scan'208"; a="226807:sNHT25476750" Received: from deskpro16133.dynamic.sanger.ac.uk ([172.19.32.236]) by intmail1b.internal.sanger.ac.uk with esmtp (Exim 4.41) id 1G4ygv-00009g-0i; Mon, 24 Jul 2006 12:33:41 +0100 Received: by deskpro16133.dynamic.sanger.ac.uk (Postfix, from userid 205) id CBAAF32C0EB; Mon, 24 Jul 2006 12:33:40 +0100 (BST) Date: Mon, 24 Jul 2006 12:33:40 +0100 From: James Bonfield To: Asim Siddiqui Message-ID: <20060724113340.GU17306@cbi1.sanger.ac.uk> References: <86C6E520C12E52429ACBCB01546DF4D3E95ECE@xchange1.phage.bcgsc.ca> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <86C6E520C12E52429ACBCB01546DF4D3E95ECE@xchange1.phage.bcgsc.ca> User-Agent: Mutt/1.5.9i X-Mailman-Approved-At: Mon, 24 Jul 2006 10:28:23 -0700 Cc: Matthew Bainbridge , Vladimir Alekseyev , trace@ncbi.nlm.nih.gov, Rene Warren , church@ncbi.nlm.nih.gov, clive.Brown@solexa.com, ssrformat@bcgsc.ca, Aaron Quinlan , Steven Jones , "Du, Lei" , Michael Stromberg , flicek@ebi.ac.uk, Gabor Marth Subject: [Ssrformat] CAF format X-BeenThere: ssrformat@mail.bcgsc.ca X-Mailman-Version: 2.1.3 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 24 Jul 2006 11:33:46 -0000 Hi all, Some notes on the CAF format. I know Gabor is tasked with sending information around about this, which is appropriate as he's an author on the CAF paper, but the primary source code is here at the Sanger Institute so I thought I'd send some quick links around: Source: http://www.sanger.ac.uk/Software/formats/CAF/ See the menu on the left for "caftools", "gap2caf" and maybe "mini phrap2gap" for example intergation to assemblers. Paper: http://www.genome.org/cgi/content/full/8/3/260 James -- James Bonfield (jkb@sanger.ac.uk) A Staden Package developer: https://sourceforge.net/projects/staden/ From marth@bc.edu Mon Jul 24 12:49:39 2006 Return-Path: X-Original-To: ssrformat@bcgsc.ca Delivered-To: ssrformat@bcgsc.ca Received: from gotland.bcgsc.bc.ca (gotland.bcgsc.bc.ca [10.9.208.74]) by mail.bcgsc.bc.ca (Postfix) with ESMTP id 5A216F000058; Mon, 24 Jul 2006 12:49:39 -0700 (PDT) Received: from mrlbva.bc.edu (HELO bc.edu) ([136.167.2.120]) by gotland.bcgsc.bc.ca with ESMTP; 24 Jul 2006 12:49:31 -0700 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AQAAANO/xESCeYdNAQEJAgwNHQ X-IronPort-AV: i="4.07,176,1151910000"; d="pdf'?scan'208,217"; a="228919:sNHT135893310" Received: from [136.167.48.109] (account marth@mail.bc.edu HELO marthsibmx60s) by fe1.bc.edu (CommuniGate Pro SMTP 5.0.9) with ESMTPSA id 148824936; Mon, 24 Jul 2006 15:49:26 -0400 From: "Gabor Marth" To: "'James Bonfield'" , "'Asim Siddiqui'" , "'Vladimir Alekseyev'" , "'Steven Jones'" , , , "'Aaron Quinlan'" , "'Michael Stromberg'" , "'Du, Lei'" , , "'Rene Warren'" , "'Matthew Bainbridge'" , , Date: Mon, 24 Jul 2006 15:50:58 -0400 Message-ID: <001b01c6af5a$7d9741a0$1cffa788@bc.edu> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_001C_01C6AF38.F685A1A0" X-Mailer: Microsoft Office Outlook 11 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2869 Thread-Index: AcavFQWdZoAnI7LAQMOlz3J4nWT43QAOKdUQ In-Reply-To: <20060724113340.GU17306@cbi1.sanger.ac.uk> X-Mailman-Approved-At: Mon, 24 Jul 2006 12:50:57 -0700 Cc: 'Gabor Marth' Subject: [Ssrformat] RE: CAF format X-BeenThere: ssrformat@mail.bcgsc.ca X-Mailman-Version: 2.1.3 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 24 Jul 2006 19:49:42 -0000 This is a multi-part message in MIME format. ------=_NextPart_000_001C_01C6AF38.F685A1A0 Content-Type: multipart/alternative; boundary="----=_NextPart_001_001D_01C6AF38.F685A1A0" ------=_NextPart_001_001D_01C6AF38.F685A1A0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hello All, Aaron, Michael, and I have talked things over after the conference call. Here are some points / suggestions that we would like to bring up / make. I have also attached the PDF of the CAF paper we have talked about during the call. Comments regarding READ (TRACE) formats. T1. Separating experimental information, archival data, and markup: It seems that there are three types of information relevant to individual sequence traces: (1) experimental conditions e.g. DNA template description such as organism, DNA type (clonal, diploid, clonally amplified diploid DNA (Solexa, 454), pooled DNA. Other mundane info such as machine ID, experiment date, reagent batch ids, etc... (2) core machine data i.e. signal intensities for nucleotides (Sanger including Solexa) or flows (454). (3) markup data i.e. base calls, quality values, mapping between called bases and flows that produced them (454); alternative base representations (e.g. we use base number probabilities corresponding to each flow). and experimental conditions; markup data (base calls); assembly (alignment) data with alignment level markups (1) + (2) are archival data that should not change after the experiment. The markup data (3) is a function of 3rd party interpretation of (1) and (2) and will change. We propose to keep all three in separate files, or at least keep the markup information separate from archival information. T2. Formats for single read and large collection of reads: A single format can be used for a single read to an entire run (maybe even multiple runs given that several runs may be part of a single experiment such as sequencing a whole genome?) T3. Representing base calls and base quality: In terms of markup, we would like a great deal of flexibility in the format to include haploid AND diploid (or even pooled DNA) base calls, and base confidence values that do not conform to the PHRED base quality value paradigm (e.g. for 454 reads are a strong case for this). T4. Intended generality of the new read format: What is the generality of the format we are hashing out? Will this be specific to "short" reads, or also include traditional "long" Sanger reads? This group would like to see an inclusive format. T5. Unique sequence IDs: Would the bigger group see value in developing standard mechanisms for the assignment of unique trace identifiers (assigned by each machine, for "new" sequences), and perhaps "retrofitted" for existing sequences in the trace archive (e.g. using the existing ABI_THUMBPRINT for ABI machines)? Comments regarding ASSEMBLY (or ALIGNMENT) formats: I have attached the CAF paper from Genome Research in 1998 for your reading pleasure. Although I am not sure whether or not we would want to stick to the specific format it proposes, it is a good starting point to remind us of the type of questions we need to consider when spec-ing out a new, more general format. Specifically, see point A2. A1. De novo vs. anchored assembly guided by a reference genome: Our new assembly format should be prepared not only for de novo assemblies but to assemblies in re-sequencing projects where the assembly is guided by and existing reference genome sequence (call this "anchored assembly"). This distinction has ramification e.g. for some of the CAF tools that don't deal with anchored assemblies (e.g. when the reference sequence has an insertion relative to EVERY aligned read). A2. Representing alignment between each read and the consensus: An important consideration will be to represent the alignment of each read to the assembled consensus sequence (in the case of a de novo assembly) or to the reference sequence (in the case of an anchored assembly). This amounts to reporting the locations of gaps of one sequence relative to the other. CAF has a reasonably efficient representation by reporting a list that consists of the "ungapped" parts of the alignment between consensus and read (in contrast with the ACE format which included each "gapped" read). BTW, we would like to see a distinction between "alignment gap" and "insertion" characters... A3. Heterogeneous trace types within a single assembly: It is already a need to assemble reads from different machine types together. We need some allowance in our format to distinguish between reads of various machine types. This would be useful both from an algorithmic and from the viewer applications' perspective. A4. Indexing on the assembly level: In our practice we have a need for "random access" not only to specific reads but of contigs, or even specific ranges of contig positions. For example, in a human re-sequencing situation, if we would like to process a specific 100kb genome region for SNP discovery, we do not want to read the whole assembly. The consensus position specific indexing may not realistic, but we would like to bring this up to other opinions. Best wishes, Gabor ================================================ Gabor T. Marth, D.Sc. Voice: 617.552-3571 Assistant Professor Lab: 617.552-0397 Department of Biology Fax: 617.552-2011 Boston College Email: marth@bc.edu Room 415 Higgins Hall 140 Commonwealth Avenue, Chestnut Hill, MA 02467 Web pages: http://bioinformatics.bc.edu/marthlab ================================================ -----Original Message----- From: James Bonfield [mailto:jkb@sanger.ac.uk] Sent: Monday, July 24, 2006 7:34 AM To: Asim Siddiqui Cc: Vladimir Alekseyev; Steven Jones; flicek@ebi.ac.uk; clive.Brown@solexa.com; Gabor Marth; Aaron Quinlan; Michael Stromberg; Du, Lei; church@ncbi.nlm.nih.gov; Rene Warren; Matthew Bainbridge; ssrformat@bcgsc.ca; trace@ncbi.nlm.nih.gov Subject: CAF format Hi all, Some notes on the CAF format. I know Gabor is tasked with sending information around about this, which is appropriate as he's an author on the CAF paper, but the primary source code is here at the Sanger Institute so I thought I'd send some quick links around: Source: http://www.sanger.ac.uk/Software/formats/CAF/ See the menu on the left for "caftools", "gap2caf" and maybe "mini phrap2gap" for example intergation to assemblers. Paper: http://www.genome.org/cgi/content/full/8/3/260 James -- James Bonfield (jkb@sanger.ac.uk) A Staden Package developer: https://sourceforge.net/projects/staden/ ------=_NextPart_001_001D_01C6AF38.F685A1A0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable