ABySS¶
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.
Usage¶
To run the default 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 running on 96 cores across 2 ddy nodes using MPI:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe parallel 96
#$ -l infiniband=ddy-i
#$ -l h_rt=240:0:0
module load abyss
abyss-pe --directory=output k=25 np=${NSLOTS} \
name=test in=reads1.fastq reads2.fastq