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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

BBMap

BBMap is part of the BBTools suite, a collection of fast tools for DNA and RNA-seq data. In addition to the bbmap.sh short-read aligner, the suite includes tools such as bbduk.sh (adapter/quality trimming and filtering), reformat.sh (format conversion), bbmerge.sh (read merging) and many others.

License

Free to use and open source under the BSD 3-Clause (LBNL) license.

Available

  • Roihu: 39.59, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load bbmap/39.59

The BBTools programs are individual shell scripts, for example:

bbmap.sh in=reads.fq ref=genome.fa out=mapped.sam
bbduk.sh in=reads.fq out=clean.fq ref=adapters.fa ktrim=r k=23 mink=11 hdist=1

The module sets the BBMAP_RESOURCES environment variable, which points to the bundled reference files such as adapter and contaminant sequences (for example $BBMAP_RESOURCES/adapters.fa).

The BBTools scripts try to detect the available memory automatically, which on a shared cluster node can request more than you reserved. On Roihu you should set the Java heap size explicitly with -Xmx to match your Slurm memory reservation, and set the number of threads with threads=.

Example batch script

#!/bin/bash
#SBATCH --job-name=bbduk
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=02:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load bbmap/39.59

bbduk.sh -Xmx15g threads=$SLURM_CPUS_PER_TASK \
    in=reads.fq out=clean.fq \
    ref=$BBMAP_RESOURCES/adapters.fa ktrim=r k=23 mink=11 hdist=1

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.

Support

CSC Service Desk

More information