[Biopython-dev] samtools threaded daemon

Christian Brueffer christian at brueffer.de
Thu Apr 11 06:10:06 UTC 2013

On 4/11/13 4:57 , Chris Mitchell wrote:
> 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
> parts.

Hi Chris,

sounds great!  I use samtools/pysam a lot, so I'd appreciate another
option.  My collegue uses mpileup with pysam a lot as well, I'm sure he
wouldn't mind some speedup in that area.



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