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


  • 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.
    • 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-2

 To see what versions of ABySS are available and if there is more than one, which is the default, along with some help, type

module spider abyss

To use ABySS, include a command like this in your batch script or interactive session to load the ABySS module: (note ‘module load’ is case-sensitive):

module load ABySS

Example script

Here is a sample script for ABySS. You can also find this script in directory /opt/packages/examples/ABySS on Bridges-2.


#SBATCH -t 10:00
#SBATCH -o abyss-example.out

module load ABySS

# echo commands to stdout
set -x

wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gz
tar xzvf test-data.tar.gz
abyss-pe k=25 name=test in='test-data/reads1.fastq test-data/reads2.fastq'