minibwa
minibwa is a short-read aligner by Heng Li, billed as the successor of BWA-MEM. It indexes a reference genome with an FM-index and aligns single- or paired-end reads using a banded, SIMD-accelerated Smith-Waterman extension, adapting its parameters to the read length. Like BWA-MEM it indexes the genome before alignment.
License
The minibwa source is released under the MIT license.
Note that the default build (as installed here) compiles the GPL-2.0+ BWT-construction
code inherited from BWA, so the installed minibwa binary is effectively GPL.
Available
- Roihu-CPU: 0.7, via the
bio-appsmodule.
Usage
minibwa is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the minibwa module:
minibwa has two subcommands, index and map.
Indexing a reference
Index the reference genome before aligning. Work in your project's /scratch
directory rather than $HOME, which is often too small for complete genomes:
This writes the index files ref.fa.l2b and ref.fa.mbw next to the reference.
Aligning reads
Paired-end reads are aligned with two read files, producing SAM on standard output:
A single read file aligns single-end:
Add -f to emit PAF instead of SAM:
Example batch script
#!/bin/bash
#SBATCH --job-name=minibwa
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=12:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=8G
module load bio-apps/v202603
module load minibwa/0.7
# Index the reference genome (once)
minibwa index -t $SLURM_CPUS_PER_TASK ref.fa
# Align paired-end reads
minibwa map -t $SLURM_CPUS_PER_TASK ref.fa read1.fq read2.fq > aln.sam
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.