BBTools

BBTools is a collection of 90+ bioinformatics tools for DNA/RNA analysis.

Availability

Cluster	Module/Version
BOSE	bbtools/39.70
BGSC	N/A

Note: You can simply use module load bbtools to activate the most recently installed version of this software.

Arguments / Options

This is a list of tools for the bbtools command that we wanted to highlight. Look at the project docs for a full list.

Option	Description
bbduk.sh	Adapter Trimming
bbmap.sh	Read Mapping
tadpole.sh	Error Correction

Sample Slurm Script

submit.sh

#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]

# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32     # How many CPU cores do you want to request
#SBATCH --nodes=1                # How many nodes do you want to request

# -- SCRIPT COMMANDS -- #

# Load the needed modules
module load bbtools/39.70                                              # Load BBTools module

# Execute a test run of BBTools using # of CPU cores requested from Slurm.
# Input files not provided.
bbmap.sh ref=reference.fasta in=reads.fq out=mapped.sam --threads=$SLURM_NTASKS

Real Example

Has your research group used BBTools in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Please include the following citation in your papers to support continued development of CheckM2.

Bushnell, B. (2014) BBMap: A Fast, Accurate, Splice-Aware Aligner.

BBTools official website: https://bbmap.org GitHub: https://github.com/bbushnell/BBTools