[BioPython] Reading Roche 454 binary SFF files in Python
Chris Fields
cjfields at illinois.edu
Fri Apr 17 12:18:53 UTC 2009
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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