[khmer] Optimization for 50bp SE reads

C. Titus Brown ctb at msu.edu
Tue Feb 18 20:31:08 PST 2014

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.

C. Titus Brown, ctb at msu.edu

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