[Biopython-dev] [Biopython (old issues only) - Bug #2905] Short read alignment format SAM / BAM

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Wed Nov 9 05:11:55 UTC 2016

Issue #2905 has been updated by Vincent Davis.

Need to review this a bit more. It looks like the primary purpose of the issue has been addressed.

Bug #2905: Short read alignment format SAM / BAM

* Author: Osvaldo Zagordi
* Status: New
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: Not Applicable
* URL: 
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)?


SamBamIO.py (9.06 KB)

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