Search results

22 items matching your search terms.
Filter the results.
Item type























New items since



Sort by relevance · date (newest first) · alphabetically
Software Project text/x-asm ABySS
by Anthony Raymond published Feb 05, 2008 last modified Jun 09, 2017 01:30 PM
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
Located in Platforms / Bioinformatics / GSC Software Centre
Software Release ABySS 1.3.5
by Anthony Raymond published Mar 05, 2013 last modified Mar 05, 2013 03:51 PM
This release introduces new tools to merge overlapping read pairs, layout and merge contigs with perfect sequence overlap, and calculate contig contiguity and correctness metrics. Also, it includes updates to the existing documentation, bug fixes, and attempts to fill scaffold gaps with a consensus of all paths between contigs.
Located in Platforms / / ABySS / Releases
Software Release ABySS 1.3.6
by Anthony Raymond published Jul 31, 2013
ABYSS and ABYSS-P are now ~20% faster. Fixed many portability issues and bugs, and improved some error messages.
Located in Platforms / / ABySS / Releases
Software Release ABySS 1.3.7
by Anthony Raymond published Dec 11, 2013 last modified Dec 12, 2013 11:40 AM
Scaffolds can now be rescaffolded using long sequences such as RNA-Seq assemblies produced from Trans-ABySS. Added support for gcc 4.8+ and Mac OS X 10.9 Mavericks with clang. Finally, we've licensed ABySS under GPL for non-commercial purposes. Please read the LICENSE file for more details.
Located in Platforms / / ABySS / Releases
Software Release ABySS 1.5.0
by Anthony Raymond published May 01, 2014
In this release we have added full strand specific RNA-Seq support such that output contigs are correctly oriented with respect to the original transcripts sequenced. Also, there are new parameters to abyss-pe, xtip and Q, that are used to improve assembly in high coverage regions like highly expressed transcripts. Setting xtip=1 will more aggressively remove certain tips. The 'Q' parameter will prevent low quality bases from being used in the assembly. The version has been bumped to 1.5.0 to signify compatibility with Trans-ABySS 1.5.0.
Located in Platforms / / ABySS / Releases
Software Release ABySS 1.5.1
by Anthony Raymond published May 08, 2014
In this release we fix a compatibility issue with Trans-ABySS 1.5.0 where the output of abyss-filtergraph is not strand-specific. Also, we include additional FCC portability fixes.
Located in Platforms / / ABySS / Releases
Software Release ABySS 1.5.2
by Anthony Raymond published Jul 10, 2014
In this release we introduce Konnector, a fast and memory-efficient tool to fill the gap between paired-end reads. Konnector determines the intervening sequence by building a Bloom filter de Bruijn graph and searching for paths between paired-end reads within the graph. A companion tool called abyss-bloom is also provided which can be used to construct reusable bloom filter files for input to Konnector; otherwise, Konnector will build an in-memory Bloom filter for one-time use. In addition to Konnector, we have fixed bugs related to compiling with GCC 4.8+ and parsing BWA output SAM files.
Located in Platforms / / ABySS / Releases
Software Release KLEAT 1.0
by Anthony Raymond published Mar 28, 2014 last modified Mar 28, 2014 05:25 PM
Initial release of CLEAT
Located in Platforms / / KLEAT / Releases
Software Project Troff document KLEAT
by Anthony Raymond published Mar 28, 2014 last modified Feb 05, 2016 10:03 AM
c(K)LEavage site Analysis of Transcriptomes (KLEAT) identifies 3' UTR ends of transcripts in de novo RNA-Seq assemblies.
Located in Platforms / Bioinformatics / GSC Software Centre
Downloadable File application/x-apple-diskimage Mac OS X package (Intel Core i3 or better)
by Anthony Raymond last modified Mar 05, 2013 04:37 PM
Located in Platforms / / Releases / ABySS 1.3.5