HMASM
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.
Protocols and Tools
