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ABySS is a parallel, paired-end sequence assembler that is designed for short reads. It is implemented using MPI and is capable of assembling large genomes.

ABySS is available as a module on Apocrita.


To run the latest installed version of ABySS, simply load the abyss module:

$ module load abyss
$ ABYSS --help

Usage:   Usage: ABYSS -k<kmer> -o<output.fa> [OPTION]... FILE...
         Assemble the input files, FILE, which may be in FASTA, FASTQ,
         qseq, export, SAM or BAM format and compressed with gz, bz2 or xz.

For full usage documentation, run ABYSS --help.

Example job

Parallel Job

Here is an example job using 64 cores:

#$ -cwd
#$ -j y
#$ -pe parallel 64
#$ -l infiniband=nxv
#$ -l h_rt=1:0:0

module load abyss

abyss-pe --directory=output k=25 np=${NSLOTS} \
name=test in=reads1.fastq reads2.fastq