Bwa

Introduction

Heng Li's aligner.

Usage

As with samtools, bwa also went through some re-structuring, so that it has an old-style tw-step (aln and sam{s,p}e) usage, characterised by the following typical sequence of commands:

bwa index reference.fa
bwa aln -I -t 8 reference.fa s_1.txt > out.sai
bwa samse reference.fa out.sai s_1.txt > out.sam
samtools view -bSu out.sam | samtools sort -  out.sorted

And then a more modern usage which consists of just one step: bwa mem.

Indexing

When bwa indexes a reference, it will use the whole filename and generate output index files with extensions added onto this name.