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.

BBMap

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