[Biopython-dev] [Bug 2905] New: Short read alignment format
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Mon Aug 24 15:21:07 UTC 2009
http://bugzilla.open-bio.org/show_bug.cgi?id=2905
Summary: Short read alignment format
Product: Biopython
Version: 1.51
Platform: All
OS/Version: Mac OS
Status: NEW
Severity: enhancement
Priority: P2
Component: Main Distribution
AssignedTo: biopython-dev at biopython.org
ReportedBy: osvaldo.zagordi at bsse.ethz.ch
Hi again,
is there any plan to develop some parsers for alignment of short reads? There's
a lot of formats around, and the most serious proposal for a format I've seen
is SAM (http://samtools.sourceforge.net/). I should start writing something to
parse this output soon. Any suggestion on where to start from (in order not to
depend on some module that will be soon obsolete)?
Thanks,
Osvaldo
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