ABySS (Assembly By Short Sequences)  is a parallel assembler for short read sequence data.

Sample scripts for ABySS use are available in directory /opt/packages/examples/abyss on Bridges.


  • User Guide
  • Web site
  • Publications:
    • 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 ResearchPubMed)
    • 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)


Usage on Bridges


To see what versions of ABySS are available type

module avail abyss

To see what other modules are needed, what commands are available and how to get additional help type

module help  abyss

To use ABySS, include a command like this in your batch script or interactive session to load the ABySS module:

module load abyss


Be sure you also load any other modules needed, as listed by the module help abyss command.