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.
License
Free to use and open source under GNU AGPLv3.
Available
- Roihu-CPU: 8.0.4, via the
bio-appsmodule.
Usage
antiSMASH is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the antiSMASH module:
Databases
antiSMASH needs reference databases. CSC provides them in
/dataset/project_2020345/antismash, and the antismash module sets the
ANTISMASH_DB environment variable to this directory. antiSMASH does not read the
variable itself, so give it with the --databases option:
CSC keeps the shared databases up to date, so you don't need to run
download-antismash-databases yourself.
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 $ANTISMASH_DB \
--output-dir results \
genome.gbk
Replace <project> with your CSC project (for example project_2001234).
See creating a batch job script for Roihu for more information about running batch jobs.