BWA

Official website : https://bio-bwa.sourceforge.net/

1 Available version
2 Job submission script
- 2.1 index
- 2.2 align

Available version

Version	Module

Version	Module
0.7.17	BWA/0.7.17-cpeGNU-23.03

Job submission script

index

#!/bin/bash
#SBATCH -p compute      # specific partition (compute,memory)
#SBATCH -N 1 -c 16      # -N 1 must be 1, -c can be 4, 8, 16, 32, 64 depending on the requirement
#SBATCH -t 24:00:00     # job time limit <hr:min:sec>
#SBATCH -A lt200xxx     # project ID
#SBATCH -J bwa-index    # job name

module restore
module load BWA/0.7.17-cpeGNU-23.03

bwa index ref.fasta

align

#!/bin/bash
#SBATCH -p compute     # specific partition (compute,memory)
#SBATCH -N 1 -c 128    # -N 1 must be 1, -c can be 4, 8, 16, 32, 64 depending on the requirement
#SBATCH -t 24:00:00    # job time limit <hr:min:sec>
#SBATCH -A lt200xxx    # project ID
#SBATCH -J bwa-align   # job name

module restore
module load BWA/0.7.17-cpeGNU-23.03

bwa mem -t $SLURM_CPUS_PER_TASK ref.fasta read1.fastq read2.fastq > aln-pe.sam