antiSMASH

antiSMASH (antibiotics and Secondary Metabolite Analysis Shell) performs genome-wide identification, annotation and analysis of secondary-metabolite biosynthesis gene clusters in bacterial and fungal genomes.

antiSMASH

License

Free to use and open source under GNU AGPLv3.

Available

Roihu: 8.0.4, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load antismash/8.0.4

Databases

antiSMASH requires reference databases that are not bundled with the module.

Shared reference databases

CSC plans to provide shared reference databases at a central location on Roihu. This is still being set up. Until it is available, download your own copy as shown below.

Download the databases to a writable location (for example your project's /scratch directory) with download-antismash-databases, and point antiSMASH at them with the --databases option:

download-antismash-databases --database-dir /scratch/<project>/antismash_db

Running antiSMASH

antiSMASH takes an annotated genome (GenBank/EMBL) or a FASTA sequence as input. It can use several CPU cores with the --cpus option. Runs should be submitted as batch jobs:

#!/bin/bash
#SBATCH --job-name=antismash
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=08:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4G

module load bio-apps/v202603
module load antismash/8.0.4

antismash --cpus $SLURM_CPUS_PER_TASK \
    --databases /scratch/<project>/antismash_db \
    --output-dir results \
    genome.gbk

Replace <project> with your CSC project (for example project_2001234), and use the same project in the database path.

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

Support

CSC Service Desk