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QIIME allows analysis of high-throughput community sequencing data
Supplementary Figure 1 Overview of the analysis pipeline. Supplementary Table 1 Details of conventionally raised and conventionalized mouse samples. Supplementary Discussion Expanded discussion ofExpand
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PyNAST: a flexible tool for aligning sequences to a template alignment
Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API). Expand
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Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community's functional capabilities. HereExpand
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Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
High-throughput sequencing has revolutionized microbial ecology, but read quality remains a considerable barrier to accurate taxonomy assignment and α-diversity assessment for microbial communities.Expand
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Human gut microbiome viewed across age and geography
Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecalExpand
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Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community ampliconExpand
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Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, theExpand
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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) andExpand
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Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions forExpand
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Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities
QIIME (canonically pronounced “chime”) is a software application that performs microbial community analysis. It is an acronym for Quantitative Insights Into Microbial Ecology, and has been used toExpand
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