The HMP performed whole metagenomic shotgun sequencing (mwgs) on over 1200 samples collected from 15-18 body sites from 300 healthy human subjects. For more detail, see Microbiome Analyses. Here we provide access to raw mwgs sequence data in fastq format.

A subset of these samples were described in a series of 2012 publications in Nature and PLoS. This subset consisted of 764 samples, comprising 16 body sites, and over 35 million human contaminant-screened reads. 749 samples were assembled using SOAPdenovo v.1.04, generating 48.3 million scaffolds.

Reads and assemblies were subjected to QC assessment, including identification of outliers by mean contig & ORF density, human hits, rRNA hits and size. 690 samples passed this QC and were included in downstream wgs analyses.

See the list of 690 samples that passed QC here.

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