Burrows-Wheeler Aligner (BWA)

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.

Website: http://bio-bwa.sourceforge.net

Three algorithms:

  • BWA-backtrack (Illumina reads up to 100bp)
  • BWA-SW (reads 70 to 1Mbp)
  • BWA-MEM (reads 70 to 1Mbp)


$git clone https://github.com/lh3/bwa.git


$sudo apt-get install bwa

Alignment (2 steps)

Step 1 – Index the reference FASTA file

$bwa index ref.fasta

Step 2 – The alignment (BWA-MEM algorithm)

$bwa mem ref.fasta reads.fastq > aln.sam
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