ABySS

Legacy documentation This page describes a service provided by a retired ACENET system. Most ACENET services are currently provided by national systems, for which please visit https://docs.computecanada.ca.

Description

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.

Modulefile

abyss

Documentation

ABySS homepage

Our current installation has the maximum k-mer length "maxk" set to 76.

Usage

Here is an example of a submission script:

#$ -cwd
#$ -l h_rt=01:00:00
#$ -pe openmp 4

module purge
module load gcc openmpi/gcc abyss
abyss-pe k=25 name=test se=test_reads.fa

Known problems

There are problems with some test jobs spanning multiple hosts, so we currently advise using the openmp parallel environment.