BWA - 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.

To run this software interactively in a Linux environment run the commands:
module load bwa

For each of the BWA algorithms, you must first index the genome with the following command:

bwa index [options] input.fasta
BWA programs may also be submitted to a queue using PBS script such as the one below:
#PBS -l nodes=2:ppn=8,pmem=1000mb,walltime=8:00:00
#PBS -m abe

module load bwa
bwa index input.fasta
bwa aln -t $PBS_NP input.fasta input.fq > output.sai
Note the use of -t $PBS_NP; this option is used to specify the number of threads used by BWA.
A list of options is available at the BWA manual page.
To run the BWA-backtrack alignment algorithm, use any of the following commands:
bwa aln
bwa samse
bwa sampe
The BWA-SW algorithm can be run using
bwa bwasw
The BWA-MEM algorithm can be run using
bwa mem

A complete list of options for each of the algorithms is available at the BWA manual page.

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