Partitioning with khmer is not my recommended approach any more

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

Our review of the eigengenome partitioning paper

Below is our first review of the paper Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning by Brian Cleary et al., recently published in Nature Biotech.

All in all, this is one of the most technically interesting papers we've read in a while.

A few interesting tidbits …

There are comments.

The Story Behind "Tackling soil diversity with the assembly of large, complex metagenomes"

I'm pleased to announce the publication of "Tackling soil diversity with the assembly of large, complex metagenomes", by Adina Howe, Janet Jansson, Stephanie Malfatti, Susannah Tringe, James Tiedje, and myself. The paper is openly available on the PNAS Web site here (open access).

External links:

Joint Genome Institute press release …

There are comments.

Page 1 / 1

Living in an Ivory Basement Stochastic thoughts on science, testing, and programming.

Other articles

Our review of the eigengenome partitioning paper

The Story Behind "Tackling soil diversity with the assembly of large, complex metagenomes"