I'm starting to work on a grant renewal for khmer, and with a lot of help from the community, including most especially Richard Unna-Smith, I've put together the following blurb. Suggestions for things to rearrange, highlight or omit welcome, as well as suggestions for things to add. I can't make …
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Note: at the Lab for Data Intensive Biology, We're trying out a new journal club format where we summarize our thoughts on the paper in a blog post. For this blog post, Camille wrote the majority of the text and the rest of us added questions and comments.
Inanç Birol …
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Last week we wrote five blog posts about some previously un-publicized features in the khmer software - most specifically, read-to-graph alignment and sparse graph labeling -- and what they enabled. We covered some half-baked ideas on graph-based error correction, variant calling, abundance counting, graph labeling, and assembly evaluation.
It was, to be …
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One of our long-term interests has been in figuring out what the !$!$!#!#%! assemblers actually do to real data, given all their heuristics. A continuing challenge in this space is that short-read assemblers deal with really large amounts of noisy data, and it can be extremely hard to look at assembly …
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De Bruijn graph alignment should also be useful for exploring concepts in transcriptomics/mRNAseq expression. As with variant calling graphalign can also be used to avoid the mapping step in quantification; and, again, as with the variant calling approach, we can do so by aligning our reference sequences to the …
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There's an interesting and intuitive connection between error correction and variant calling - if you can do one well, it lets you do (parts of) the other well. In the previous blog post on some new features in khmer, we introduced our new "graphalign" functionality, that lets us align short sequences …
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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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