Suppose you have a community that has two organisms in it, at widely varying abundances. What can you do?
Partitioning takes this mixed distribution and, based on graph connectivity, splits the reads into two bins. Thus, you go from this:
to this:
where the reads are …
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This is the story behind our PNAS paper, "Scaling Metagenome Assembly with Probabilistic de Bruijn Graphs" (released from embargo this past Monday).
Why did we write it? How did it get started? Well, rewind the tape 2 years and more...
There we were in May 2010, sitting on 500 million …
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(updated to point to http://arxiv.org/).
Authors: Jason Pell, Arend Hintze, Rosangela Canino-Koning, Adina Howe, James M. Tiedje, C. Titus Brown
Abstract:
The memory requirements for de novo assembly of short-read shotgun sequencing data from complex microbial populations are an increasingly large practical barrier to environmental studies. Here we …read more
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I'm writing this on my way back from Stockholm, where I attended a workshop on the 4th Paradigm. This is the idea (so named by Jim Gray, I gather?) that data-intensive science is a distinct paradigm from the first three paradigms of scientific investigation -- theory, experiment, and simulation. I was …
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This blog post was inspired by two recent events.
First, in response to a NY Times article about the "data deluge" affecting biologists, one of my Facebook friends said something like "stop whining about how hard it is to analyze the data and do some good experiments instead!" I vehemently …
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I'm just on my way back from a JGI workshop on metagenome informatics, and I thought I'd take the opportunity to write up a short review.
The workshop was, frankly, excellent. We saw a bunch of talks on metagenome assembly (my current interest) as well as single-cell sequencing approaches, and …
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(with Adina Howe, Jason Pell, Rosangela Canino-Koning, and Arend Hintze).
A few weeks ago I blogged a bit about a k-mer filtering system, khmer, that we were using to reduce metagenomic data to a more tractable size by throwing out error-prone reads (see A memory efficient way to remote …
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