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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.


  • Module bwa-0.7.15: BWA version 0.7.15, 64-bit, parallel version
  • Module bwa-0.7.13: BWA version 0.7.13, 64-bit, parallel version
  • Module bwa-0.7.3a: BWA version 0.7.3a, 64-bit, parallel version
  • Module 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 (ppn attribute) reserved
$ qsub -I -l nodes=1:ppn=X -l mem=Yg
Note: Do not forget to apppropriately set the amount of requested memory (mem attribute) 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



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]

Supported platforms


Program administrator

Tom Rebok