NIH Human Microbiome Project 2

HMP Data Release Phase 1

Nature (2012) doi:10.1038/nature11209

flowchart Body site specific assemblies (HMBSA) Read level functional profiling Clustered gene indices (HMGC) GO Slim results (HMGS) Clustering GO category categorization Hybrid gene indices (HMHGI) Gene prediction, annotation QIIME community profiling (HMQCP) Bacterial reference genome strain selection Mock Community Mock community  16S & WGS reads (HMMC) Genes of interest (HMGOI) All processed and annotated 16S (HM16STR) QIIME HMP Reference genomes 16S Strain repository WGS Archaeal, bacterial, eukaryotic and viral genomes IMG/HMP dbGaP Public Archive HMP Archive WGS & 16S HMP Project Catalog Bacterial genome annotation NCBI St. Louis Houston Mothur community profiling (HMMCP) Mothur Alignment Chimera checking RDP classification Raw 16S data and library metadata (HMR16S) Biological samples WUGI JCVI Broad BCM Library construction metadata Human sequence Removal Library construction, sequencing Phenotype and Sample Metadata Sample metadata Participant phenotype metadata EMMES Quality control, sample review and release Gene Indices (HMGI) Gene prediction, annotation Recovery of unassembled reads, body site specific assembly Metabolic reconstructions and clusters (HMMRC) Non-redundant species selection Shotgun community profiling (HMSCP) Quality control, sample review and release QC and sample review 12 Hybrid assemblies (HMHASM) Newbler-based Hybrid assembly generation 454 WGS  Reads, 17 samples (HM4WGS) Read level genome alignment 3,096 Reference  genomes (HMREFG) Functional databases: KEGG, other (HMFUNC) Read level metabolic profiling 749 Assemblies (HMASM) SOAP-based assembly generation Deduplication, trimming, QC evaluation Illumina WGS Reads, 764 Samples (HMIWGS) Reference genomes Figure Legend