GSC Software Centre

ABySS 1.2.2

Shaun Jackman — 2010-08-25T19:28:19Z

2010-08-25 Shaun Jackman

Release version 1.2.2.
Merge contigs after popping bubbles.
Handle multi-line FASTA sequences.
Report the amount of memory used.
Most tools can output their results in SAM format, including AdjList, KAligner, ParseAligns and PathOverlap.

abyss-pe

New command, se-dot. Output a Graphviz dot file of the single-end assembly.

ABYSS

Handle multi-line FASTA sequences.
Report the amount of memory used.
Improve error messages for incorrectly-formatted FASTA files.
Bug fix. Improved handling of palindromes.

PopBubbles

Merge contigs after popping bubbles.
Bug fix. Do not pop bubbles resulting from palindromes.

KAligner

Report the amount of memory used.
New option, --sam. Output the alignments in SAM format.

ParseAligns, DistanceEst

Bug fix. The CIGAR string was oriented with respect to the query rather than with respect to the target, which is standard.

AdjList, PathOverlap

New option, --sam. Output the adjacency graph in SAM format.

abyss-fixmate

New program. Similar to samtools fixmate, but does not require that the input be sorted by query ID, although it is faster if it is sorted.

SSAKE 3.6

Rene Warren — 2010-08-25T16:10:00Z

SSAKE v3.6 accepts various size length sequence libraries. To work with paired data from libraries of different template sizes, users must now add ":template_size" (e.g. >SLXA23-1-1-2-13:200 for a 200bp library) at the end of the input file header (>) for each pairs. v3.6 also has preliminary support for Sanger, paired-end reads.

MiRNA Profiling 0.2.5

Andy Chu — 2010-08-05T22:46:45Z

This releases contains a major bug fix in reporting star strand miRNAs introduced in v0.2.4's new annotations.

MiRNA Profiling 0.2.4

Andy Chu — 2010-07-19T21:55:00Z

This release fixes some major bugs in the coordinate based annotation of miRNA arms and the tracking of cross-mapped miRNAs. Annotations are also improved with more detail.

ABySS 1.2.1

Shaun Jackman — 2010-07-12T21:35:00Z

2010-07-12 Shaun Jackman

    * Release version 1.2.1.
    * Handle reverse-forward oriented mate pair libraries.
    * Improved distance estimates, particularly with large fragment
    libraries.

    abyss-pe:
    * New commands:
    se-contigs: Assemble single-end contigs.
    pe-contigs: Assemble paired-end contigs (default).
    se-sam: Output a gzipped SAM file of the single-end assembly.
    se-bam: Ouptut a BAM file of the single-end assembly.
    pe-dot: Output a Graphviz dot file of the paired-end assembly.
    all: Sam as se-bam pe-contigs pe-dot.
    * Options for one particular library may be specified:
    lib='lib1 lib2' lib2_s=1000 lib2_n=25
    * Input sequence may come from an arbitrary command, which is
    useful to assemble a region of an aligned BAM file:
    in='<(samtools view genome.bam chr10)'

    ABYSS:
    * Bug fix. When reading SAM/BAM files, the quality format
    incorrectly defaulted to ASCII-64, when it should be ASCII-33.

    ABYSS-P:
    * May use the Intel MPI library.

    ParseAligns:
    * Count the number of forward-reverse, reverse-forward and
    forward-forward oriented alignments.

    DistanceEst:
    * Handle reverse-forward oriented mate pair libraries.
    * Improved distance estimates, particularly with large fragment
    libraries.
    * Remove duplicate mate pairs.
    * Print a pretty UTF-8 bar plot of the fragment-size distribution.
    * Multithreaded using OpenMP. The -j, --threads option specifies
    the number of threads to use.
    * Performance improvment.

    Overlap:
    * Handle cases when more than one gap occurs within the mate pair
    fragment size.

    SimpleGraph:
    * Performance improvment.

    MergePaths:
    * Handle the case when a circular sequence is assmembled into a
    single contig.

    abyss-tofastq:
    * New program. Convert qseq, export, SAM and BAM files to FASTA or
    FASTQ format. The files may be compressed with gz, bz2 or xz and
    may be tarred.

MiRNA Profiling 0.2.2

Andy Chu — 2010-06-02T01:02:16Z

First public release.

ABySS-Explorer 1.0.1

Cydney Nielsen — 2010-06-02T00:15:00Z

Fixed bug causing errors when loading some ABySS graphs.

SSAKE 3.5

Rene Warren — 2010-05-28T14:54:24Z

In v3.5, the read pairing logic is used in the extension process. More specifically, passed the upper bound insert size, only forward reads AND reverse reads having their assembled mate already assembled in the contig being built will be considered for extension. This has for effect to mitigate contig misassemblies due to repeats. It will also extend the end of adjacent contigs in a scaffold in an effort to fill gaps - the resulting contigs are placed in the .mergedcontigs file.

ABySS 1.2.0

Kevin Teague — 2010-05-26T18:30:00Z

2010-05-25 Shaun Jackman

* Release version 1.2.0.
* Scaffold over gaps in coverage and unresolved repetitive
sequence using Ns.
* Read sequence from SAM and BAM files.

abyss-pe:
* Set q=3 by default. Trim bases from the ends of reads whose
quality is less than 3.
* Do not store the .pair.gz file.
* Generate a BAM file of the mate pairs that align to
different contigs of the single-end assembly. Disabled by default.
* Output a Graphviz dot file of the paired-end assembly.
Disabled by default.
* Store the bubbles in ${name}-bubbles.fa rather than bubbles.fa.
* Store the indel bubbles in ${name}-indel.fa.
* Bug fix for mawk.

ABYSS:
* Set -E0 when coverage is low (<2).

ABYSS-P:
* Remove the temporary files contigs-*.fa and snp-*.fa.

PopBubbles:
* Output in Graphviz dot format using --dot.

KAligner:
* Do not ignore sequences (reads or contigs) containing N.
* Output SAM headers (but not SAM alignments).

ParseAligns:
* Output in SAM format.

DistanceEst:
* Input in SAM format.
* Output in Graphviz dot format using --dot.

Overlap:
* Scaffold over gaps in coverage. Scaffolding can be disabled
using the option --no-scaffold.
* Merge contigs that overlap at simple repeats. These merges can
be prevented using the option --no-merge-repeat.

SimpleGraph:
* Scaffold over repeats. Scaffolding can be disabled using the
option --no-scaffold.

MergePaths:
* Merge paths containing ambiguous sequence.
* Multithreaded using OpenMP. The -j, --threads option specifies
the number of threads to use.

MergeContigs:
* Merge paths and contigs containing ambiguous sequence.

PathOverlap:
* Output in Graphviz dot format using --dot.

Consensus:
* Output the pileup in samtools format.

Trans-ABySS 0.2

Kevin Teague — 2010-05-26T18:10:00Z

Addition of scripts for novel poly-adenylation site detection and novel anomalous contig detection.

Trans-ABySS 0.1

Readman Chiu — 2010-04-14T18:25:55Z

Initial Trans-ABySS release.

ABySS-Explorer 1.0

Cydney Nielsen — 2010-02-26T23:46:34Z

Initial ABySS-Explorer release.

ABySS 1.1.2

Shaun Jackman — 2010-02-15T18:19:06Z

2010-02-15 Shaun Jackman

* Release version 1.1.2.

ABYSS:
* Read tar files including compressed tar files.
* New parameter -b, --bubble-length=N. Pop bubbles shorter than
N bp. The default is b=3*k.

AdjList:
* Include the contig coverage in the output.
* The script abyss-adjtodot converts an ABySS adjacency file to
GraphViz dot format.

PopBubbles:
* Pop bubbles resulting from indels.

KAligner:
* Synchronize the threads periodically (every ten thousand
alignments by default) to ease the computational burden on
ParseAligns. This synchronization can be disabled using --sync=0.
* Use two threads by default.

abyss-pe:
* New parameter, b.
* Use two threads by default.
* The read length argument, l, is deprecated. To emulate the
behaviour of ABySS 1.0.14 and older, set t=6*(l-k+1). The default
is t=k.

ABySS 1.1.1

Shaun Jackman — 2010-01-20T00:03:17Z

2010-01-19 Shaun Jackman

* Release version 1.1.1.

ABYSS:
* Pop complex bubbles either completely or not at all. Bubble
popping now completes in a single round.
* Choose better (typically lower) default values for the
parameters -e,--erode and -c,--coverage. The default threshold is
the square root of the median k-mer coverage.

ABySS 1.1.0

Shaun Jackman — 2009-12-21T19:36:46Z

2009-12-18 Shaun Jackman

* Release version 1.1.0.
* The output format of AdjList, DistanceEst and SimpleGraph has
changed.

ABYSS:
* New options, -q, --trim-quality. Trim bases from the ends of
reads whose quality is less than the specified threshold.
--standard-quality: zero quality is `!' (33)
default for FASTQ files
--illumina-quality: zero quality is `@' (64)
default for qseq and export files
Thanks to Tony Raymond.

SimpleGraph:
* Multithreaded. The -j, --threads option specifies the number of
threads to use.
* Expand tandem repeats when it is possible to determine the exact
number of the repeat.

MergePaths:
* Bug fix. A repeat that is larger than the fragment size could
be misassembled. Thanks to Tony Raymond.

abyss-pe:
* Determine the parameter j (number of threads) by finding the
number of slots allocated on the head node in the PE_HOSTFILE.
* Store the k-mer coverage histogram in coverage.hist.