One of the biggest problems with basic sequence analysis -- some would say the biggest problem -- is the error rate. If our sequencing reads were error-free, both assembly and mapping would be much, much easier. Alas, Illumina reads have a 0.1-1% error rate per base, and PacBio has an error …
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I'm at the MBL STAMPS course, "Strategies and Techniques for Analyzing Microbial Population Structure," and one of the things I needed to address in my morning talk was the role that the k parameter plays in de Bruijn graph assemblers.
In most de Bruijn assemblers that I have used -- Velvet …
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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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I've just posted my 2nd try at the NSF CAREER award to the lab Web site, where it joins my recent NSF BIGDATA proposal, my Moore Foundation proposal, last year's (rejected) NSF CAREER proposal, my NGS course grant, and my one big funded grant, my USDA proposal from 2009. The …
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Data and materials availability All data necessary to understand, assess, and extend the conclusions of the manuscript must be available to any reader of Science. All computer codes involved in the creation or analysis of data must also be available to any reader of Science. After publication, all reasonable …read more
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