One of the newer features in khmer that we're pretty excited about is the read-to-graph aligner, which gives us a way to align sequences to a De Bruijn graph; our nickname for it is "graphalign."
Briefly, graphalign uses a pair-HMM to align a sequence to a k-mer graph (aka De …
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About a month ago, I took some time to try out Docker, a container technology that lets you bundle together, distribute, and execute applications in a lightweight Linux container. It seemed neat but I didn't apply it to any real problems. (Heng Li also tried it out, and came to …
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After a fair amount of time thinking about software's place in science (see blog posts 1, 2, 3, and 4), and thinking about khmer's short- and long-term future, we're making some changes to our development process.
Semantic versioning: The first change, and most visible one, is that we are going …
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I finally got a chance to more thoroughly read Mark Stalzer and Chris Mentzel's arxiv preprint, "A Preliminary Review of Influential Works in Data-Driven Discovery". This is a short review paper that discusses concepts highlighted by the 1,000+ "influential works" lists submitted to the Moore Foundation's Data Driven Discovery …
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We just finished teaching the second of my RNAseq workshops at UC Davis -- the fifth workshop I've hosted since I took a faculty position here in VetMed. In order, we've done a Train the Trainers, a Data Carpentry, a reference-guided RNAseq assembly workshop, a mothur (microbial ecology) workshop, and a …
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Note - this was an internal funding request solicited by the Center for Open Science. It's been funded!
Brief: We propose to integrate OSF into Galaxy as a data store. For this purpose, we request 3 months of funding (6 months, half-time) for one developer, plus travel.
Introduction and summary: Galaxy …
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