[BioPython] Reading Roche 454 binary SFF files in Python

[Martin MOKREJŠ]

Hi,

Peter wrote:
> On Wed, Apr 15, 2009 at 10:01 AM, Jose Blanca <jblanca at btc.upv.es> wrote:
>>>> The main problem would be to have sff files small enough to be used
>>>> for the test.
>>> The Roche command line tools allow you to take a large SFF file and
>>> produce a filtered version (use sfffile with the -i option and a simple
>>> text file of read identifiers).  So making a small SFF file for unit tests
>>> should be simple.
>> Could you send a couple of example sff files to me?
>>
> 
> I'm not sure what SFF data I would be allowed to distribute, especially if
> you want it for a publicly available unit test example.  Once the analysis

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