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.
bwa-0.7.15: BWA version 0.7.15, 64-bit, parallel version
bwa-0.7.13: BWA version 0.7.13, 64-bit, parallel version
bwa-0.7.5a: BWA version 0.7.3a, 64-bit, parallel version
bwa-0.7.3a: BWA version 0.7.3a, 64-bit, parallel version
bwa-0.6.2: BWA version 0.6.2, 64-bit, parallel version
1. Running the application -- Interactive mode:
- ask the scheduler for an interactive job having a single node and a desired number of processors (
$ qsub -I -l nodes=1:ppn=X -l mem=Yg
- Note: Do not forget to apppropriately set the amount of requested memory (
memattribute) and/or another job requirements.
- load the Moses module
$ module add bwa-0.7.3a
- prepare the configuration and the input files and run the computation
$ bwa [index|samse|sampe] <options> # just single-threaded versions $ bwa [aln|bwasw] -t $PBS_NUM_PPN <options> # ALN and BWASW support multi-threaded/parallel processing
2. Running the application -- Batch mode:
- prepare the job description script -- use a general skeleton supplemented by the following lines:
... # load the BWA module module add bwa-0.7.3a # run the computation bwa [index|samse|sampe] <options> # just single-threaded versions bwa [aln|bwasw] -t $PBS_NUM_PPN <options> # ALN and BWASW support multi-threaded/parallel processing ...
- pass the job description file to the scheduler together with (at least) the requested number of processors and requested amount of memory
$ qsub -l nodes=1:ppn=X -l mem=Yg mydescriptionfile.sh
- online at producer's webpage
$ man bwa
The full BWA package is distributed under GNU General Public License version 3 as it uses source codes from BWT-SW which is covered by GPL. Sorting, hash table, BWT and IS libraries are distributed under the MIT license.
- If you use the short-read alignment component, please cite the following paper:
- Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-60. [PMID: 19451168]
- If you use the long-read component (BWA-SW), please cite:
- Li H. and Durbin R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. [PMID: 20080505]