ABySS...

Overview

ABySS (Assembly By Short Sequences) 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.

ABySS is developed in the Canada's Michael Smith Genome Sciences Centre supervised by Dr Inanc Birol.

How to use

Check if abyss is installed and if it is, then what versions are available:

$ module avail abyss

We recommend using the latest version. Always load a module for specific version. Example:

$ module load abyss/2.2.3

For more details on using modules see software applications guide.

Here's an example PBS script that will work with sample data downloaded from here :

#!/bin/bash

#PBS -q normal
#PBS -l ncpus=2
#PBS -l mem=4GB
#PBS -l walltime=00:30:00
#PBS -l wd

# Must include `#PBS -l storage=scratch/ab12+gdata/yz98` if the job
# needs access to `/scratch/ab12/` and `/g/data/yz98/`

# Load modules, always specify version number.
module load openmpi/4.1.0
module load abyss/2.2.3

abyss-pe np=2 k=31 name=Sample_Kmer31 in="test-data/reads1.fastq test-data/reads2.fastq"

Note that this job will use time allocations from default project. To change it to other project, use #PBS -P <projcode> directive.

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How to use

Authors: Javed Shaikh, Mohsin Ali