bwa
Link to section 'Introduction' of 'bwa' Introduction
BWA (Burrows-Wheeler Aligner) is a fast, accurate, memory-efficient aligner for short and long sequencing reads.
For more information, please check its website: https://biocontainers.pro/tools/bwa and its home page: http://bio-bwa.sourceforge.net.
Link to section 'Versions' of 'bwa' Versions
- 0.7.17
Link to section 'Commands' of 'bwa' Commands
- bwa
- qualfa2fq.pl
- xa2multi.pl
Link to section 'Module' of 'bwa' Module
You can load the modules by:
module load biocontainers
module load bwa
Link to section 'Example job' of 'bwa' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run BWA on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bwa
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers bwa
bwa index ref.fasta
bwa mem ref.fasta input.fq > test.sam