ABySS ("Assembly By Short Sequences") is a de novo, parallel, paired-end sequence assembler.

The ABySS home page is at http://www.bcgsc.ca/platform/bioinfo/software/abyss.

Available modules

Packages with modules

Module NeSI Cluster
ABySS/2.0.2-gimkl-2017a pan
ABySS/2.0.1-foss-2015a pan

Licensing requirements

ABySS is made available at no cost for non-commercial use under the terms of version 3 of the GNU General Public Licence or, at the option of the user, any later version of the same licence. Researchers intending to use ABySS for commercial purposes should contact Patrick Rebstein. For more details, including the full text of the licence, please consult the LICENSE file located in the share/doc/abyss subdirectory of the ABySS installation directory.

Example scripts

Example script for the Pan cluster

#!/bin/bash -e

#SBATCH --job-name        ABySS_job
#SBATCH --account         nesi99999
#SBATCH --time            01:00:00
#SBATCH --mem-per-cpu     4G
#SBATCH --nodes           1 
#SBATCH --ntasks-per-node 12
#SBATCH --output          ABySS_job.%j.out # Include the job ID in the names
#SBATCH --error           ABySS_job.%j.err # of the output and error files

module load ABySS/2.0.1-foss-2015a

# This example specifies --ntasks-per-node and --nodes rather than the usual 
# --ntasks because, when given multiple CPUs, ABySS runs both MPI and non-MPI 
# parallel sub-programs.  It does its own MPI launching and so should not be 
# started via srun.
# See https://github.com/bcgsc/abyss#parallel-processing for details.

abyss-pe name=ecoli k=64 in='reads1.fa reads2.fa'
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