Burrows-Wheeler Alignment (BWA)
Description
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.
Version
- 0.7.12
Authorized Users
CIRCE
account holdersRRA
account holdersSC
account holders
Platforms
CIRCE
clusterRRA
clusterSC
cluster
Modules
Burrows-Wheeler Alignment (BWA) requires the following module file to run:
apps/bwa/0.7.12
- See Modules for more information.
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 --cpus-per-task=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 30 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:
#!/bin/bash # #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
Documentation
Home Page, User Guides, and Manuals
- BWA Home Page:
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