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.
Packages with modules
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
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'