[BioPython] Reading Roche 454 binary SFF files in Python

[Chris Fields]

Just to add, Pjotr Prins' BioLib initiative (http://biolib.open-bio.org/wiki/Main_Page 
) is building SWIG-based interfaces to several C/C++-based libraries,  
including Staden io_lib, which supports the following formats (c&p  
from the latest io_lib README):

	SCF trace files
	ABI trace files
	ALF trace files
	CTF trace files
	ZTR trace files
	SFF trace archives
	SRF trace archives
	Experiment files
	Plain text files

We're working on the Perl/Ruby bindings; it shouldn't be hard at all  
to get Python (and by extension, Biopython) working.

chris

On Apr 17, 2009, at 7:06 AM, Peter wrote:

> On Wed, Apr 15, 2009 at 11:04 AM, Martin MOKREJŠ
> <mmokrejs at ribosome.natur.cuni.cz> wrote:
>> Hi,
>> ...
>> Just some random links to NCBI Trace Archive:
>>
>> ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead
>> http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=table&f=study&m=data&s=study
>> http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP000001 (has  
>> 454 data from 2007)
>> http://www.ncbi.nlm.nih.gov/sites/entrez?db=sra&report=full&term=SRX003639
>> ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/sff2scf/sff2scf.tar.gz
>>
>> Hope this helps,
>> Martin
>
> Thanks for those links Martin,
>
> I've use a FASTQ file from that list for a couple of examples I've
> just added to the tutorial.
>
> Peter
>
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