[Bioperl-l] How to convert SFF into Fastq

[Dan Bolser]

(In theory,) the list of tools that produce and consume SFF can be found here:

http://seqwiki.org/SFF


Currently listed (and not already mentioned) is:
* http://seqwiki.org/PyroBayes

On 15 July 2010 19:40, Peter <biopython at maubp.freeserve.co.uk> 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
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