ABySS
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ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.
If you need larger kmer size please load the module abyss/1.2.7-maxk96.
To run AbySS on Kalkyl use the module system. NB! The later versions of ABySS only work with the gcc compiler. To be on the safe side. Remember to specify the versions used, not the default.
module load gcc openmpi module load bioinfo-tools abyss
Run in parallel in slurm
#!/bin/bash -l #SBATCH -J abysstest #SBATCH -o abysstest.output #SBATCH -e abysstest.error #SBATCH --mail-user smurf@smurfland.se #SBATCH --mail-type=ALL #SBATCH -t 02:00:00 #SBATCH -A b2010999 #Use one node with 8 cores #SBATCH -p node -n 8 module load gcc openmpi module load bioinfo-tools abyss/VERSION abyss-pe np=$SLURM_NPROCS ...(your options)
Publisher
Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
