[Bioperl-l] How to convert SFF into Fastq

Peter biopython at maubp.freeserve.co.uk
Thu Jul 15 14:40:05 EDT 2010

On Thu, Jul 15, 2010 at 6:53 PM, Juan Jovel <jovel_juan at hotmail.com> wrote:
> Hello!
> How can I convert a SFF file from 454 into a Fastq format?
> Thanks a lot!

I am aware of three options, none of which use Perl,

(1) Use the Roche (linux only) SFF tools (sffinfo or sfffile, I forget
which), to give you FASTA+QUAL, then using your tool of choice go to
FASTQ (e.g. BioPerl).

(2) Use the open source command line tool sff_extract (written in Python),
it can do FASTA and QUAL, and I think there is an option for FASTQ too.

(3) Use Biopython's SeqIO, e.g. the Bio.SeqIO.convert() function.

Things are more complex if you are working with paired end data...


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