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To the Editor: High-throughput sequencing is revolutionizing microbial ecology studies. Efforts like the Human Microbiome Projects 1 and the US National Ecological Observatory Network 2 are helping us to understand the role of microbial diversity in habitats within our own bodies and throughout the planet.

Pyrosequencing using error-correcting, sample-specific barcodes allows hundreds of communities to be analyzed simultaneously in multiplex 3. Integrating information from thousands of samples, including those obtained from time series, can reveal large-scale patterns that were inaccessible with lower-throughput sequencing methods. However, a major barrier to achieving such insights has been the lack of software that can handle these increasingly massive datasets. Although tools exist to perform library demultiplexing and taxonomy assignment 4, 5, tools for downstream analyses are scarce.