The HMP performed whole metagenomic shotgun sequencing on 1260 samples collected from 15-18 body sites from 300 healthy human subjects. Here we provide access to that raw wgs sequence data in fastq format.
A subset of these samples, referred to as "Phase I", were published in Nature in 2012. This subset consisted of 764 samples, comprising 16 body sites, and over 35 million human contaminant-screened reads. Of these, 749 samples underwent assembly using SOAP, generating 48.3 million scaffolds.
Reads and assemblies were subjected to QC assessment, including identification of outliers by mean contig and ORF density, human hits, rRNA hits and size. 690 Phase I samples passed this QC and were included in downstream wgs analyses.
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