So, I got this grant. And, um, it looks like khmer has a future, which means... so does my lab.
What is khmer?
khmer is my lab's software for doing various things to sequencing data, and is largely focused on providing good demo implementations of low-memory data structures …
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(This blog post was mightily helped by Qingpeng Zhang, the first author of the paper; he wrote the pipeline. I just ran it a bunch :)
We have been benchmarking k-mer counters in a variety of ways, in preparation for an upcoming paper. As with the diginorm paper we are automating …
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This post can be referenced and cited at the following DOI: http://dx.doi.org/10.6084/m9.figshare.98198.
For a few months, the Trinity list was awash with discussions about how to use digital normalization to lower the memory and compute requirements for mRNASeq assembly. At some point …
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An increasing number of people are asking about using our assembly approaches for things that we haven't yet written (or posted) papers about. Moreover, our assembly strategies themselves are also under constant evolution as we do more research and find ever-wider applicability of our approaches.
This has been moved to …
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These talk notes are for my talk at the 2012 Argonne Soil Metagenomics Workshop.
The slides are available for viewing and download here, on Slideshare.
I'm going to be talking about our assembly pipeline for soil metagenomes.
Much of this work was done by …
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This is the story behind our PNAS paper, "Scaling Metagenome Assembly with Probabilistic de Bruijn Graphs" (released from embargo this past Monday).
Why did we write it? How did it get started? Well, rewind the tape 2 years and more...
There we were in May 2010, sitting on 500 million …
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Here's a data analysis question for all you Big Data folk.
A beachcomber is interested in obtaining up to 10 examples of every type of shell present on a beach. The shells are individually easy to find, but some types are really rare and some are really abundant. The beachcomber …
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