> 2010/2/8 Charles Imbusch <[email protected]> >> Hello, >> >> I have been wondering whether Biojava is able to >> handle sff files coming from 454 sequencing runs. >> >> I found something here: >> http://lists.open-bio.org/pipermail/biojava-dev/2009-July/003907.html >> >> Does somebody know about the current status on Biojava and sff files? >> >> >> Thanks in advance, >> Charles
On Mon, Feb 8, 2010 at 9:24 PM, Paolo Pavan <[email protected]> wrote: > > Unfortunately, after spending some time on it, I didn't anything, sorry. > There is just a post more I sent to Andreas Prlic without enclose the list > by mistake, in which I report a few info more, coming from my reading on > BioPerl's way to manage contigs and assembly informations. > Nothing more. > > Paolo Hi, I've CC'd the common OpenBio mailing list as this is probably of interest beyond just BioJava. Based on code from Jose Blanca (author of sff_extract), I implemented support for the SFF (Roche 454) sequencing reads for Biopython last year on a branch that I hope to merge into our next release, currently here: http://github.com/peterjc/biopython/tree/sff-seqio In addition to the Roche Manuals (which may not be that easy to get a copy of), the SFF format is described on this NCBI webpage: http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=formats#sff I'm happy to answer questions on how the file format works (including the undocumented index block which I had to reverse engineer). Peter P.S. Just to clarify (from the old BioJava thread), the SFF file just holds the raw reads - it is an input file for doing an assembly or mapping. _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
