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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
Downloadable File Source
by Anthony Raymond last modified May 01, 2014 03:57 PM
Located in Platforms / / Releases / ABySS 1.5.0
Downloadable File Test dataset
by Anthony Raymond last modified May 01, 2014 03:58 PM
Located in Platforms / / Releases / ABySS 1.5.0
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
Downloadable File Test dataset
by Anthony Raymond last modified May 08, 2014 12:49 PM
Located in Platforms / / Releases / ABySS 1.5.1
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
Downloadable File Source
by Anthony Raymond last modified Dec 11, 2013 02:03 PM
Located in Platforms / / Releases / ABySS 1.3.7
Downloadable File Test input data (paired end reads)
by Anthony Raymond last modified Dec 11, 2013 02:04 PM
Located in Platforms / / Releases / ABySS 1.3.7
by Anthony Raymond last modified May 29, 2014 11:18 AM
Located in Platforms / / Releases / ABySS 1.5.1
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