ABySS

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Availability

Resource Centre Description
Kalkyl UPPMAX cluster resource of about 21 TFLOPS

License

License: Free.

Experts

No experts have currently registered expertise on this specific subject. List of registered field experts:
Field AE FTE General activities
Henric Zazzi (PDC) PDC Bioinformatics 100100 Bioinformatics Application support
Joel Hedlund (NSC) NSC Bioinformatics 00
Martin Dahlö (UPPMAX) UPPMAX Bioinformatics 1010 Bioinformatic support
Sebastian DiLorenzo (UPPMAX) UPPMAX Bioinformatics 5050 National bioinformatic support, NGS tumor data

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

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