BWA

module avail bwa/       # BWA
module avail bwa-mem2/  # BWA mem2

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 mem2 is the next version of the BWA-mem algorithm in BWA.

It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.

Usage

License

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]

Single- and multithread run

$ 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

Running BWA-mem2

bwa-mem2 version   # Will show the software version
bwa-mem2 index -p <prefix_name> <in_reference.fasta>
bwa-mem2 mem <prefix_name> <reads_1.fq/fa> <reads_2.fq/fa> -t $PBS_NUM_PPN > out.sam