q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data

by Nicholas A. Bokulich, Matthew R. Dillon, Yilong Zhang, Jai Ram Rideout, Evan Bolyen, Huilin Li, Paul S. Albert, J. Gregory Caporaso
Published 2018-11-01

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

by Nicholas A. Bokulich, Benjamin D. Kaehler, Jai Ram Rideout, Matthew Dillon, Evan Bolyen, Rob Knight, Gavin A. Huttley, J. Gregory Caporaso
Published 2018-05-01

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking

by Nicholas A. Bokulich, Jai Ram Rideout, William G. Mercurio, Arron Shiffer, Benjamin Wolfe, Corinne F. Maurice, Rachel J. Dutton, Peter J. Turnbaugh, Rob Knight, J. Gregory Caporaso, Josh D. Neufeld
Published 2016-10-01

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

by Jai Ram Rideout, Yan He, Jose A. Navas-Molina, William A. Walters, Luke K. Ursell, Sean M. Gibbons, John Chase, Daniel McDonald, Antonio Gonzalez, Adam Robbins-Pianka, Jose C. Clemente, Jack A. Gilbert, Susan M. Huse, Hong-Wei Zhou, Rob Knight, J. Gregory Caporaso
Published 2014-08-01