Burrows-Wheeler Alignment (BWA)


From the Burrows-Wheeler Aligner (BWA) Home Page: Burrows-Wheeler Aligner (BWA) is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.


  • 0.7.12

Authorized Users

  • CIRCE account holders
  • SC account holders


  • CIRCE cluster
  • SC cluster


Burrows-Wheeler Alignment (BWA) requires the following module file to run:

  • apps/bwa/0.7.12

Running Burrows-Wheeler Alignment (BWA) on CIRCE/SC

The Burrows-Wheeler Alignment (BWA) user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Interactive Mode

Next, use the following commands to open an SRUN Interactive Session, load the module for Burrows-Wheeler Alignment (BWA), and execute the Burrows-Wheeler Alignment (BWA) binary:

[user@login0 ~]$ srun --time=48:00:00 --nodes=1 --ntasks-per-node=1 --pty /bin/bash
[user@wh-520-4-1 ~]$ module load apps/bwa/0.7.12
[user@wh-520-4-1 ~]$ bwa

Batch Job submission

To run batch jobs on the CIRCE/SC cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than 20 minutes to run on a standard PC.

If, for example, you have a FASTQ file nsamed short_read.fq you wish to align using ref.fa, you would set up a submit script to use BWA like this:

#SBATCH --job-name=bwa-test
#SBATCH --time=48:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --output=output.%j.bwa-test

#### SLURM 1 processor BWA test to run for 48 hours.

# Load the BWA module:
module load apps/bwa/0.7.12

# Start BWA
bwa aln ref.fa short_read.fq > aln_sa.sai

Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./bwa-test.sh
  • You can view the status of your job with the “squeue -u <username>” command


Home Page, User Guides, and Manuals

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with Burrows-Wheeler Alignment (BWA) to the IT Help Desk: rc-help@usf.edu