On Tuesday, I wrote a draft blog post in response to Michael Eisen's blog post on how Lior Pachter's blog post was a a model for post-publication peer review (PPPR). (My draft post suggested that scientific bloggers aim for inclusivity by adopting a code of conduct and posting explicit site …
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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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So far, in this week of khmer blog posts (1, 2, 3), we've been focusing on the read-to-graph aligner ("graphalign"), which enables sequence alignments to a De Bruijn graph. One persistent challenge with this functionality as introduced is that our De Bruijn graphs nodes are anonymous, so we have no …
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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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