[Bioperl-l] How to convert SFF into Fastq

[Chris Fields]

On Jul 15, 2010, at 1:40 PM, Peter wrote:

> 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!
>> 
>> JUAN
> 
> 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.
> http://bioinf.comav.upv.es/sff_extract/
> 
> (3) Use Biopython's SeqIO, e.g. the Bio.SeqIO.convert() function.
> 
> Things are more complex if you are working with paired end data...
> 
> Peter

We are planning some tools for SFF work with BioPerl, possibly using BioLib's io_lib bindings.  Much of this is to replace the legacy io_lib bindings from bioperl-ext, which is essentially dead at the moment.

chris