Accessible, curated metagenomic data through ExperimentHub
Duy Tin Truong,
Jennifer Beam Dowd,
Levi D Waldron
Posted 27 Jan 2017
bioRxiv DOI: 10.1101/103085 (published DOI: 10.1038/nmeth.4468)
Posted 27 Jan 2017
We present curatedMetagenomicData, a Bioconductor and command-line interface to thousands of metagenomic profiles from the Human Microbiome Project and other publicly available datasets, and ExperimentHub, a platform for convenient cloud-based distribution of data to the R desktop. The resource provides standardized per-participant metadata linked to bacterial, fungal, archaeal, and viral taxonomic abundances, as well as quantitative metabolic functional profiles. The datasets can be immediately analyzed in R or other software with a minimum of bioinformatic expertise and no preprocessing of data. We demonstrate identification of taxonomic/functional correlations, an investigation of gut "enterotypes", and a comparison of the accuracy of disease classification from different data types. These documented analyses can be reproduced efficiently on a laptop, without the barriers of working with large-scale, raw sequencing data. The building and expansion of curatedMetagenomicData is based entirely on open source software and pipelines, to facilitate the addition of new microbiome datasets and methods.
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