1. The Critical Assessment of Metagenome Interpretation and why I'm not a fan

    Update 3/29/15: the CAMI FAQ now includes information on reproducibility measures, and looks very promising. The data sets they are producing also seem fascinating.

    If you're into metagenomics, you may have heard of CAMI, the Critical Assessment of Metagenome Interpretation. I've spoken to several people about it in …

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  2. Estimating (meta)genome size from shotgun data

    This is a recipe that provides a time- and memory- efficient way to loosely estimate the likely size of your assembled genome or metagenome from the raw reads alone. It does so by using digital normalization to assess the size of the coverage-saturated de Bruijn assembly graph given the reads …

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  3. Estimate whether your sequencing has saturated your sample to a given coverage

    This recipe provides a time-efficient way to determine whether you've saturated your sequencing depth, i.e. how much new information is likely to arrive with your next set of sequencing reads. It does so by using digital normalization to generate a "collector's curve" of information collection.

    Uses for this recipe …

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