What Does Bwa Expect In Its Alignment Database

Question

[User 8364]

I'm trying to align a large dataset of fastq reads against a reference genome, which I have as a fasta file, but it seems that bwa wants more than just a fasta file to align them.

Here's what I'm trying:

$ bwa samse /data/glycine_data/gmax_genome_data/Glyma1.cds.fa d3_1.fq d3_2.fq 
[bns_restore] fail to open file '/data/glycine_data/gmax_genome_data/Glyma1.cds.fa.ann'. Abort!
Aborted

Is there any way I can construct this .ann file that it wants?

Answer 1

[Gww]

You need to index your reference genome using bwa index prior to alignment.

For example:

bwa index /data/glycine_data/gmax_genome_data/Glyma1.cds.fa

There are some command line options for the index that you can read here.