![]() This minor release provides bug fixes and improved reliability for both MPI assemblies and Bloom filter assemblies on large datasets. (Tigmint and ARCS must be installed separately.) In addition, simultaneous optimization of `s` (seed length) and `n` (min supporting read pairs / Chromium barcodes) is now supported during scaffolding. This release adds support for misassembly correction and scaffolding using linked reads, using Tigmint and ARCS. Parallelization of Sealer has also been improved, thanks to contributions by 13, 2018 This release provides bug fixes and modest improvements to Bloom filter assembly contiguity/correctness. This release improves scaffold N50 on human by ~10%, due to implementation of a new `-median` option for `DistanceEst` (thanks to This release also adds a new `-max-cost` option for `konnector` and `abyss-sealer` that curbs indeterminately long running times, particularly at low k values. This release fixes a SAM-formatting bug that broke the ABySS-LR pipeline (Tigmint/ARCS). ![]() On human, Bloom filter assembly times are still a few hours longer than MPI assemblies (e.g. Bloom filter assemblies now have equivalent scaffold contiguity and better correctness than MPI assemblies of the same data, while still requiring less than 1/10th of the memory. This release provides major improvements to Bloom filter assembly contiguity and correctness. GitHub release page for ABySS All Releases VersionĬompiler fixes and increase stack size limits to avoid stack overflows. Gordon Robertson, Jacqueline Schein, Readman Chiu, Richard Corbett, Matthew Field, Shaun D Jackman, Karen Mungall, Sam Lee, Hisanaga Mark Okada, Jenny Q Qian, Malachi Griffith, Anthony Raymond, Nina Thiessen, Timothee Cezard, Yaron S Butterfield, Richard Newsome, Simon K Chan, Rong She, Richard Varhol, Baljit Kamoh, Anna-Liisa Prabhu, Angela Tam, YongJun Zhao, Richard A Moore, Martin Hirst, Marco A Marra, Steven J M Jones, Pamela A Hoodless Marco A Marra, Steven J M Jones, Pamela A Hoodless and İnanç Birol. De novo assembly and analysis of RNA-seq data.İnanç Birol, Shaun D Jackman, Cydney Nielsen, Jenny Q Qian, Richard Varhol, Greg Stazyk, Ryan D Morin, Yongjun Zhao, Martin Hirst, Jacqueline E Schein, Doug E Horsman, Joseph M Connors, Randy D Gascoyne, Marco A Marra and Steven JM Jones. De novo Transcriptome Assembly with ABySS.Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. ( Genome Research, PubMed)ĪBySS: A parallel assembler for short read sequence data. PublicationsĪBySS 2.0: resource-efficient assembly of large genomes using a Bloom filter. Jackman SD, Vandervalk BP, Mohamadi H, Chu J, Yeo S, Hammond SA, Jahesh G, Khan H, Coombe L, Warren RL, Birol I. Genome Research, 2017 27: 768-777. June 2015, 12th 2 Conference in Basel, Switzerland: ABySS was the winner of the Swiss Institute of Bioinformatics’ inaugural International Bioinformatics Resource Award. To assemble transcriptome data, see Trans-ABySS. The parallel version is implemented using MPI and is capable of assembling larger genomes. The single-processor version is useful for assembling genomes up to 100 Mbases in size. ![]() ![]() ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. ![]()
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