I'm at the PyCon 2015 sprints (day 2), and I took the opportunity to play around with named pipes.
I was reminded of named pipes by Vince Buffalo in this great blog post, and since we at the khmer project are very interested in streaming, and named pipes fit well …
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We just posted a new preprint (well, ok, a few weeks back)! The preprint title is "Crossing the streams: a framework for streaming analysis of short DNA sequencing reads", by Qingpeng Zhang, Sherine Awad, and myself. Note that like our other recent papers, this paper is 100% reproducible, with all …
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I've been putting together a streaming API for khmer that would let us use generators to do sequence analysis, and I'd be interested in thoughts on how to do it in a good Pythonic way.
Some background: a while back, Alex Jironkin asked us for high level APIs, which turned …
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A colleague who is starting their own computational lab just asked me for some advice on how to run software projects, and I wrote up the following. Comments welcome!
A brief summary of what we've converged on for our own needs is this:
everything's on github (you can have private …
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Michael R. Crusoe and I are throwing a sprint!
Somewhat in the vein of last year's mini-Hackathon, Michael and I and other members of the lab are going to focus in on reviewing contributions and closing issues on the khmer project for a 5 day period.
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As we think about the next few years of khmer development, it is helpful to explore what khmer is, and what our goals for khmer development are. This can provide guiding principles for development, refactoring, extension, funding requests, and collaborations.
Comments solicited!
Links:
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In Extracting shotgun reads based on coverage in the data set, we showed how to get a read coverage spectrum for a shotgun data set. This is a useful diagnostic tool that can be used to estimate total genome size, average coverage, and repetitive content.
Uses for this recipe include …
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