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Downloadable File Source code
by Ben Vandervalk last modified Sep 01, 2016 11:13 AM
Located in Platforms / / Releases / ABySS 2.0.0
Software Release ABySS 2.0.0
by Ben Vandervalk published Sep 01, 2016
This release introduces a new Bloom filter assembly mode that enables large genome assemblies with minimal memory (e.g. 34 GB for H. sapiens with 76X coverage bfc-corrected reads). Bloom filter assemblies are currently less contiguous than the default (MPI) assembly mode but are still of high quality (e.g. 3.5 Mbp vs. 4.8 Mbp scaffold NG50 for H. sapiens). Bloom filter assembly mode is enabled by adding three 'abyss-pe' parameters (B = *Bloom filter size*, H = *number of Bloom filter hash functions*, kc = *k-mer coverage threshold*). See 'README.md' for an example. This release also updates several 'abyss-pe' parameter defaults to be more suitable for large genome assemblies with recent Illumina data. In addition, ABySS 2.0.0 includes minor usability improvements for 'abyss-sealer' and removes an unnecessary build dependency on sqlite3.
Located in Platforms / / ABySS / Releases
Software Release Konnector 2.0
by Ben Vandervalk published Nov 03, 2015
First release following publication of Konnector 2.0
Located in Platforms / / Konnector / Releases
Software Release Sealer 1.9.0
by Ben Vandervalk published Nov 03, 2015
First official release of Sealer following publication.
Located in Platforms / / Sealer / Releases
by Ben Vandervalk last modified May 29, 2015 03:52 PM
Located in Platforms / / Releases / ABySS 1.9.0
Software Release ABySS 1.9.0
by Ben Vandervalk published May 29, 2015 last modified May 29, 2015 03:55 PM
This release introduces a new paired de Bruijn graph mode for assembly. In paired de Bruijn graph mode, ordinary k-mers are replaced by k-mer pairs, where each k-mer pair is separated by a fixed-size gap. The primary advantage of paired de Bruijn graph mode is that the span of a k-mer pair can be arbitrarily wide without consuming additional memory, and thus provides improved scalability for assemblies of long sequencing reads. This release also introduces a new tool called Sealer for closing scaffold gaps, new Konnector functionality for producing long pseudo-reads, and support for the DIDA (Distributed Indexing Disptached Alignment) parallel alignment framework.
Located in Platforms / / ABySS / Releases
Downloadable File Source code
by Ben Vandervalk last modified Apr 24, 2015 10:53 AM
Located in Platforms / / Releases / DIDA 1.0.1
Software Release DIDA 1.0.1
by Ben Vandervalk published Apr 24, 2015
This version introduces compression of intermediate files to reduce disk space requirements.
Located in Platforms / / DIDA / Releases
Downloadable File Test input data (paired end reads)
by Ben Vandervalk last modified Mar 05, 2013 03:47 PM
Located in Platforms / / Releases / ABySS 1.3.5
Downloadable File Test input data (paired end reads)
by Ben Vandervalk last modified Feb 04, 2013 04:41 PM
Located in Platforms / / Releases / ABySS 1.3.4