ABySS
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
Current release
ABySS 1.3.5
Released Mar 05, 2013
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.
More about this release…
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ABySS
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all platforms
(635.8 kB)
- Source
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Get
ABySS
for
all platforms
(1.4 MB)
- Test input data (paired end reads)
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ABySS
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Mac OS X
(2.7 MB)
- Mac OS X package (Intel Core i3 or better)
Project Description
ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.
To assemble transcriptome data, see Trans-ABySS.
Publications
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ABySS: A parallel assembler for short read sequence data. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. Genome Research, 2009-June. (Genome Research, PubMed)
- De novo Transcriptome Assembly with ABySS. 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. Bioinformatics. 2009-June. (Bioinformatics Advance Access) - De novo assembly and analysis of RNA-seq data. 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. Nature Methods. 2010-Oct. (Nature)
