ABySS

“ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads” (http://www.bcgsc.ca/platform/bioinfo/software/abyss).

Using ABySS with Slurm

The ABySS README covers the basics of using ABySS, but it doesn’t describe how to use it with Slurm. Here is a sample script which manipulates the sample files provided in the ABySS documentation.

#!/bin/sh
#SBATCH -N 2

# Uses tutorial and test data from ABySS GitHub README:
# https://github.com/bcgsc/abyss

. /usr/modules/init/bash
module load openmpi-apps/1.10.2/abyss/1.9.0

# The np=? parameter must match the number of nodes allocated in the SBATCH line.
abyss-pe np=2 k=25 name="test" \
    in='reads1.fastq reads2.fastq'