An initial taxonomical investigation of the genome bins.
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Comparing genome sets extracted from metagenomes (Sunday Morning Bioinformatics).
A post about k-mers - this time for taxonomy!
A (revised and updated) shotgun metagenome workshop at UC Santa Cruz
We just finished teaching a second version of our two-day shotgun metagenome analysis workshop, this time at UC Santa Cruz (the first one was in October 2016, at Scripps Institute of Oceanography). Harriet Alexander led the workshop and Phillip Brooks and I co-taught; Luiz Irber, Shannon Joslin, and Taylor Reiter …
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Advancing metagenome classification and comparison by MinHash fingerprinting of IMG/M data sets.
This is our just-submitted proposal for the JGI-NERSC "Facilities Integrating Collaborations for User Science" call. Enjoy!
- Brief description: (Limit 1 page)
Abstract: Sourmash is a command-line tool and Python library that calculates and compares MinHash signatures from sequence data. Sourmash "compare" and "gather" functionality enables comparison and characterization of signatures …
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A shotgun metagenome workshop at the Scripps Institute of Oceanography
We just finished teaching a two day workshop at the Scripps Institute of Oceanography down at UC San Diego. Dr. Harriet Alexander, a postdoc in my lab, and I spent two days going through cloud computing, short read quality and k-mer trimming, metagenome assembly, quantification of gene abundance, mapping of …
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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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