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Accessible, curated metagenomic data through ExperimentHub

Research output: Contribution to journalArticlepeer-review

Edoardo Pasolli, Lucas Schiffer, Paolo Manghi, Audrey Renson, Valerie Obenchain, Duy Tin Truong, Francesco Beghini, Faizan Malik, Marcel Ramos, Jennifer Beam Dowd, Curtis Huttenhower, Martin Morgan, Nicola Segata, Levi Waldron

Original languageEnglish
JournalNATURE METHODS
Accepted/In press1 Aug 2017

Documents

  • NatureMethods_17

    NatureMethods_17.pdf, 696 KB, application/pdf

    Uploaded date:04 Sep 2017

    Version:Submitted manuscript

    Licence:CC BY-NC

King's Authors

Abstract

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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