1. Summary of Amazon Rainforest Microbial Observatory shotgun read assembly

    (with Adina Howe, James Tiedje, Titus Brown)

    I have been working on the assembly of big shotgun metagenomic data from ARMO (Amazon Rain Forest Microbial Observatory) project. The biggest challenge is the huge data size, 2TB in fastq and more than 6 billions reads after read trimming. One lucky thing …

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  2. A mildly crazy idea: crowdsourced -omic analysis with data privacy sunset?

    Or, "can we crowdsource BGI?" ;)

    With all of the crazy need surrounding genomic analysis -- most of it on a shoestring budget -- I am thinking about a mildly crazy idea.

    What if I offered to computationally analyze people's non-model transcriptomic and metagenomic data for them, in exchange for (a) non-exclusive access …

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  3. A simple idea: standard but optional review criteria for bioinformatics papers

    Brad Chapman (@chapmanb on twitter) wrote and signed a nice review of my submission to the Bioinformatics Open Source Conference. In his review, he said

    My only small suggestion is to include some discussion about your
    reproducibility work during the talk: the Amazon AMI, documentation
    and reproducible ipython workflows. This …
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