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

Nicholas A. Bokulich, Benjamin D. Kaehler, Jai Ram Rideout, +5

Microbiome

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

Daniel McDonald, José C. Clemente, Justin Kuczynski, +9

GigaScience

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

Evan Bolyen, Jai Ram Rideout, Matthew R. Dillon, +105

Qiime 2DysbiosisEngineeringBiological DatabaseData Science +12

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

Evan Bolyen, Jai Ram Rideout, Matthew R. Dillon, +106

Qiime 2DysbiosisEngineeringBiological DatabaseData Science +12

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

Jai Ram Rideout, Yan He, José A. Navas-Molina, +13

PeerJ

Cluster ComputingEngineeringOpen-reference Otu PickingGeneticsGenomics +24

Temporal variability is a personalized feature of the human microbiome

Gilberto E. Flores, J. Gregory Caporaso, Jessica B. Henley, +9

Genome biology

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

Nicholas A. Bokulich, Matthew R. Dillon, Yilong Zhang, +5

mSystems

The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites

Luke K. Ursell, José C. Clemente, Jai Ram Rideout, +3

Journal of Allergy and Clinical Immunology

Microbial DiversityMicrobiome BiologyDysbiosisMicrobiotaHuman-associated Microbiota +6

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

Evan Bolyen, Jai Ram Rideout, Matthew R. Dillon, +106

Qiime 2DysbiosisEngineeringBiological DatabaseData Science +12

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity

Yan He, J. Gregory Caporaso, Xiaotao Jiang, +8

Microbiome