BWA
Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements three algorithms, BWA-MEM (mem), BWA-Backtrack (aln) and BWA-SW (bwasw). BWA-Backtrack works for query sequences shorter than 200 bp. The other two algorithms are used for longer reads up to around 100 kbp. BWA-MEM is recommended for reads longer than 70 bp. All algorithms do gapped alignment.
BWA can be used to align both single-end and paired-end reads to a reference genome or sequence set.
License
Free to use and open source under GNU GPLv3.
Available
- Roihu: 0.7.19, via the
bio-appsmodule.
Usage
BWA is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the BWA module:
The basic syntax of BWA commands is:
BWA indexes
The first step in aligning with BWA is downloading the reference genome and indexing it. Note that your $HOME directory is often too small for working with complete genomes; you should do the analysis in the scratch directory of your project instead.
Download a reference genome (for example with wget) to your scratch directory, then calculate the BWA indexes for it:
Note that for small (less than 2 GB) reference genomes you could use the faster "is" indexing algorithm (bwa index -a is).
Single-end alignment
Once the indexing is ready you can carry out the alignment for single-end reads with the command:
If you wish to use the aln (BWA-Backtrack) algorithm, you need to do the alignment in two steps.
First calculate the actual alignment:
The result file is in BWA-specific .sai format that you can convert to SAM format with the bwa samse command:
Paired-end alignment
If you use the MEM algorithm, you can do the paired-end alignment with just one command:
In the case of the BWA-Backtrack algorithm, you should first do a separate alignment run for each read file:
bwa aln Homo_sapiens.GRCh38.dna.toplevel.fa reads1.fq > aln1.sai
bwa aln Homo_sapiens.GRCh38.dna.toplevel.fa reads2.fq > aln2.sai
The two .sai alignment files are combined with the bwa sampe command:
Example batch script
BWA jobs should be run as batch jobs. Below is a sample batch job script for running a BWA job on Roihu:
#!/bin/bash
#SBATCH --job-name=bwa
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --account=<project>
#SBATCH --partition=small
#SBATCH --time=12:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4000M
module load bio-apps/v202603
module load bwa/0.7.19
# Index the reference genome
bwa index -a bwtsw Homo_sapiens.GRCh38.dna.toplevel.fa
# Run the alignment
bwa mem -t $SLURM_CPUS_PER_TASK Homo_sapiens.GRCh38.dna.toplevel.fa reads1.fq reads2.fq > aln.sam
In the batch job example above, one BWA task (--ntasks=1) is executed. The BWA job uses 8 cores (--cpus-per-task=8) with a total of 32 GB of memory. The maximum duration of the job is twelve hours (--time=12:00:00). All the cores are assigned from one computing node (--nodes=1). Replace <project> with your CSC project (for example project_2001234).
You can submit the batch job file to the batch job system with the command:
See creating a batch job script for Roihu for more information about running batch jobs.
Support
More information
More information about BWA can be found from: