BWA - file formats

[robekubica]

Hello,

I have some basic questions about BWA file formats:

- Which are the file formats that Burrows-Wheeler Alignment Tool (BWA) admit as input?
- Is ab1 admited?
- How could I use BWA if my sequences are in ab1, or CTF(Staden Package) or SCF(Staden Package) format?

Thanks a lot

[swbarnes2]

Hello,

I have some basic questions about BWA file formats:

- Which are the file formats that Burrows-Wheeler Alignment Tool (BWA) admit as input?
- Is ab1 admited?
- How could I use BWA if my sequences are in ab1, or CTF(Staden Package) or SCF(Staden Package) format?

Thanks a lot

I'm pretty sure bwa only takes fasta or fastq. You'll have to convert those other things to fasta, but that shouldn't be too hard.