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