There's been a lot of discussion about PyCon talks that we do want to see. Here's a brief list of those I don't want to see, for those of you considering a submission -- in no particular order.
There are comments.
[ Note: I wrote the following e-mail to the Microbiology (MMG) department faculty mailing list here at MSU. I'll post any interesting responses that I get. --titus ]
---
Hi all,
I'm an unabashed proponent of Open Access publishing, as well as the idea of decoupling correctness from estimated impact of a paper …
read moreThere are comments.
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 …
read moreThere are comments.
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 …
read moreThere are comments.
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 …
There are comments.
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 …
read moreThere are comments.