Published: Wed 20 January 2016
By C. Titus Brown
In science .
tags: khmer partitioning
I wrote the below in response to someone who e-mailed me about
trying out our partitioning approach for metagenome assembly.
yes, the original partitioning approach worked only on low coverage
data sets. The main reason is that highly connected regions (repeats,
from biology; and some kinds of sequencing errors) are incredibly hard
to traverse.
Our 2014 paper
used a modified protocol, which included both digital normalization
and a "knot removal" approach. This should work, but...
...since then, we've continued to refine the approach, but it's not something
we're actively working on. A big part of the reason is that there are
some nifty new metagenome assemblers that resolve most of the problems
we set out to solve -- MEGAHIT is the one that we recommend.
If you're interested in genome separation/binning/strain extraction on
raw reads, the Cleary et al. 2015 paper is
where I would look. I wrote a News and Views piece on it.
The leading edge of technology in metagenomics keeps on moving. Exciting
times ;).
--titus
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