bacteria genome mapping using bwa

Question

[hirakuda]

Please someone suggest how to use bwa to map bacteria genomes to a sample? I want to use bwa mem. I did something bwa mem bacteria ref original sample > align.mem.out. and got some error. I dont know whether I am using it correctly. Can someone please suggest the correct command to use bwa to map severel bacteria together?

[Fatima]

What is the error?

First you need to create an index for your bacterial genome reference.

Then you can align your sample(s) to the reference genome.

bwa index ref.fa

bwa mem ref.fa reads.fq > aln-se.sam

samtools view -S -b aln-se.sam > aln-se.bam

Note that the output format is not .out

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

http://quinlanlab.org/tutorials/samtools/samtools.html