[Biopython-dev] samtools threaded daemon

Chris Mitchell chris.mit7 at gmail.com
Thu Apr 11 02:57:41 UTC 2013

Hi everyone,

I've been doing a ton of mpileup work recently with samtools so I made a
python daemon to parallelize the process.  Is there any interest in a
generic SamTools package for BioPython?  I know pysam exists, but it'd be
an added dependency as well as not threaded.  In my experience, for
querying a ton of positions threading mpileup is the best way to go (much
faster than -l bed_file in my use cases).  If there's interest, I'll
package it as a general SamTools command line wrapper with the added
bonuses that for certain operations you can input a list and thread those


More information about the Biopython-dev mailing list