Sometimes you've really got to wonder.
The Chronical of Higher Ed just posted this article on a collaboration between A. Sean Pue, Tracy K. Teal, and myself. It's about bringing bioinformatics (or, really, CS and computational linguistics) to the study of Urdu poetic meter.
The article has two interesting flaws …
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So, there this guy, Matt Welsh. And he left Harvard to go to Google. OK.
Now he's baaaack, to point out that academia isn't that rosy.
Yep. He's not wrong.
Were I in a sarcastic mood, I would say something like "ohmigod, Matt Welsh is pointing out that …
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I was a reviewer of the PLoS One paper, An Integrated Pipeline for de Novo Assembly of Microbial Genomes, and just recently came across the review again. I didn't post it at the time, but heck, why not now? ;)
Note that for our recent microbial genomes assembly workshop we wrote …
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Is khmer evolving?
The khmer project is our software package to work with short reads, and it enables a lot of things like k-mer counting and de Bruijn graph exploration and modification. As data volume grows, interest in partitioning and digital normalization is also growing. But we haven't really talked …
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Continuing in the saga of "what do sequencing errors do to our de Bruijn graph density measure" (read the first post here), I have some new results.
The conclusion of the first post was that on random (non-real) genomes, both with and without repeats, we see that de Bruijn graph …
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Are our reviewers correct or incorrect?
About two months ago we got back reviews for our assembly artifacts paper, in which we showed that there was a strong 3' bias in the reads towards higher graph connectivity. Since shotgun sequencing is supposed to be random, we asserted that this 3' …
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