[khmer] Optimization for 50bp SE reads

[C. Titus Brown]

On Tue, Feb 18, 2014 at 08:29:41PM -0800, Elizabeth Trembath-Reichert wrote:
> Would you suggest any khmer optimizations for 50bp SE reads from what is
> listed for the data processing examples here?
> 
> https://khmer-protocols.readthedocs.org/en/latest/metagenomics/

Hi Elizabeth,

the only trick is that you'll have to modify various instructions to
only deal with single-ended reads.  It actually dramatically simplifies
the protocol, but we don't have a clear path to single-end assembly
written down anywhere... it's not impossible to adapt but please ask
us if you have any questions.

No change to processing parameters in particular, though.

best,
--titus
-- 
C. Titus Brown, ctb at msu.edu