ABySS

ABySS (Assembly By Short Sequences) is a de novo sequence assembler designed for short paired-end reads and genomes of all sizes. It supports memory-efficient Bloom-filter assembly and a legacy MPI mode.

ABySS

License

Free to use and open source under GNU GPLv3.

Available

Roihu: 2.3.10, via the bio-apps module.

Usage

ABySS is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the ABySS module:

module load bio-apps/v202603
module load abyss/2.3.10

Assemblies are run with the abyss-pe driver. A minimal paired-end assembly uses a k-mer size (k), an output name (name) and the input reads (in):

abyss-pe k=64 B=2G name=assembly in='reads1.fq.gz reads2.fq.gz'

For larger assemblies, ABySS recommends Bloom-filter mode, enabled by setting the B memory budget. The appropriate value of B depends primarily on genome size. MPI mode is still available but is considered legacy upstream.

Example batch script

Assembly jobs are resource demanding and should be run as batch jobs. Below is a sample multithreaded batch job script using Bloom-filter mode:

#!/bin/bash
#SBATCH --job-name=abyss
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=12:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4G

module load bio-apps/v202603
module load abyss/2.3.10

abyss-pe k=64 B=2G j=$SLURM_CPUS_PER_TASK \
    name=assembly \
    in='reads1.fq.gz reads2.fq.gz'

Replace <project> with your CSC project (for example project_2001234).

You can submit the batch job file to the batch job system with the command:

sbatch batch_job_file.sh

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk