Using Bfast To Align Illumina Paired End Reads

Question

[Travis]

Hi,

I am attempting to use Bfast to align some paired-end Illumina reads. The problem is that the forward and reverse reads come in separate files and Bfast doesn't seem to explicitly account for this anywhere. Other aligners such as BWA expect the reads in this format.

Has anyone else had success with this?

Thanks in advance.

Answer 1

[brentp]

There's a script in the BFAST scripts/ directory to do this for you: scripts/ill2fastq.pl. Something like:

perl scripts/ill2fastq.pl s_ > output.fasq

where s_ is the prefix of your reads file.

[Travis]

Cheers Brent. Wasn't sure if this was what I was looking for but it seems to be.