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

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

bwa index input_reference.fasta index_prefix

The index_prefix is then use for the actual alignment step which is as follows:

bwa mem index_prefix input_reads_pair_1.fastq input_reads_pair_2.fastq

In this case we have paired read-files. With single reads of course only one name would be required.