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Curtis Huttenhower 2016. MetaPhlAn profiling of 20 HMP samples. protocols.io https://dx.doi.org/10.17504/protocols.io.d9e93dCopy Citation Copied
URL: https://dx.doi.org/DOI:10.17504/protocols.io.d9e93d
Authors: Curtis Huttenhower
Group: VERVE Net, Huttenhower Lab
Summary: In this protocol we will show how to taxonomically profile 20 metagenomic shotgun samples Human Microbiome Project (HMP). Specifically, we will look at 10 samples from the buccal mucosa and 10 from the tongue dorsum. Please note these 20 samples are not necessarily an unbiased selection of microbiomes from the over 200 buccal mucosa and tongue dorsum samples generated by the HMP.REQUIREMENTS: BowTie2 installed and in the system path, Mercurial, basic unix commands (wget, tar).The size of the 20 samples (60GBs) can make their download quite slow. For this reason we are also providing the overall output of this protocol (few KBs) available for download so that one can start the tutorial from MetaPhlAn output merge and visualization if needed.
External URL: https://bitbucket.org/nsegata/metaphlan/wiki/MetaPhlAn_Pipelines_Tutorial
Version: 1
Publication Date: 2016
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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