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
There are comments .
Proudly powered by pelican , which uses python .
The theme is subtlely modified from one by Smashing Magazine , thanks!
For more about this blog's author, see the main site or the lab site
While the author is employed by the University of California, Davis, his opinions are his own and almost certainly bear no resemblance to what UC Davis's official opinion would be, had they any.