Data Resources

Every AWS resource listed below was confirmed available in the public HMPDACC S3 bucket on July 27, 2026.

Understanding license plates

A license plate identifies a defined HMPDACC data collection or analysis product. For each collection there is an Amazon Web Services (AWS) S3 directory containing the files or index information associated with that collection. Some current AWS directories were added after the historical license-plate system and therefore have no assigned license plate.

HMPDACC data catalog

Search or filter the catalog, then copy an S3 URI or download command directly from the matching resource.

Showing 102 of 102 resources.

Confirmed HMP and iHMP data products, public S3 directories, and BioProjects
License plate Project / study Data product Description AWS location BioProject
— HMP
Demonstration Projects
Project directory 		PRJNA46327 demonstration project directory
Multiple data types · Project collection 		BioProject title: Metagenomic study of the human skin microbiome associated with acne. HMP demonstration-project root directory for this accession; child directories organize microbiome and/or reference-genome resources where present. Access: Public s3://hmpdcc/hmp1/demo/PRJNA46327/
Download Guide
— HMP
Demonstration Projects
Project directory 		PRJNA46877 demonstration project directory
Multiple data types · Project collection 		BioProject title: The Vaginal Microbiome: Disease, Genetics and the Environment. HMP demonstration-project root directory for this accession; child directories organize microbiome and/or reference-genome resources where present. Access: Public s3://hmpdcc/hmp1/demo/PRJNA46877/
Download Guide
— HMP
Demonstration Projects
Project directory 		PRJNA46307 demonstration project directory
Multiple data types · Project collection 		BioProject title: Foregut microbiome in development of esophageal adenocarcinoma. HMP demonstration-project root directory for this accession; child directories organize microbiome and/or reference-genome resources where present. Access: Public s3://hmpdcc/hmp1/demo/PRJNA46307/
Download Guide
— HMP
Demonstration Projects
Project directory 		PRJNA46309 demonstration project directory
Multiple data types · Project collection 		BioProject title: Evaluation of the cutaneous microbiome in psoriasis. HMP demonstration-project root directory for this accession; child directories organize microbiome and/or reference-genome resources where present. Access: Public s3://hmpdcc/hmp1/demo/PRJNA46309/
Download Guide
— HMP
Demonstration Projects
Project directory 		PRJNA46879 demonstration project directory
Multiple data types · Project collection 		BioProject title: Diet, Genetic Factors, and the Gut Microbiome in Crohn's Disease. HMP demonstration-project root directory for this accession; child directories organize microbiome and/or reference-genome resources where present. Access: Public s3://hmpdcc/hmp1/demo/PRJNA46879/
Download Guide
— HMP
Demonstration Projects
Project directory 		PRJNA46317 demonstration project directory
Multiple data types · Project collection 		BioProject title: Urethral Microbiome of Adolescent Males. HMP demonstration-project root directory for this accession; child directories organize microbiome and/or reference-genome resources where present. Access: Public s3://hmpdcc/hmp1/demo/PRJNA46317/
Download Guide
— HMP
Demonstration Projects
Project directory 		PRJNA46319 demonstration project directory
Multiple data types · Project collection 		BioProject title: The Thrifty Microbiome: The Role of the Gut Microbiota in Obesity in the Amish. HMP demonstration-project root directory for this accession; child directories organize microbiome and/or reference-genome resources where present. Access: Public s3://hmpdcc/hmp1/demo/PRJNA46319/
Download Guide
— HMP
Demonstration Projects
Project directory 		PRJNA46321 demonstration project directory
Multiple data types · Project collection 		BioProject title: Metagenomic Analysis of the Structure and Function of the Human Gut Microbiota in Crohn's Disease. HMP demonstration-project root directory for this accession; child directories organize microbiome and/or reference-genome resources where present. Access: Public s3://hmpdcc/hmp1/demo/PRJNA46321/
Download Guide
— HMP
Demonstration Projects
Project directory 		PRJNA46323 demonstration project directory
Multiple data types · Project collection 		BioProject title: Effect of Crohn's Disease Risk Alleles on Enteric Microbiota. HMP demonstration-project root directory for this accession; child directories organize microbiome and/or reference-genome resources where present. Access: Public s3://hmpdcc/hmp1/demo/PRJNA46323/
Download Guide
— HMP
Demonstration Projects
Project directory 		PRJNA46331 demonstration project directory
Multiple data types · Project collection 		BioProject title: The Microbial Ecology of Bacterial Vaginosis: A Fine Scale Resolution Metagenomic Study. HMP demonstration-project root directory for this accession; child directories organize microbiome and/or reference-genome resources where present. Access: Public s3://hmpdcc/hmp1/demo/PRJNA46331/
Download Guide
— HMP
Demonstration Projects
Project directory 		PRJNA46335 demonstration project directory
Multiple data types · Project collection 		BioProject title: The Human Virome In Children And Its Relationship To Febrile Illness. HMP demonstration-project root directory for this accession; child directories organize microbiome and/or reference-genome resources where present. Access: Public s3://hmpdcc/hmp1/demo/PRJNA46335/
Download Guide
— HMP
Demonstration Projects
Project directory 		PRJNA46337 demonstration project directory
Multiple data types · Project collection 		BioProject title: The Neonatal Microbiome and Necrotizing Enterocolitis. HMP demonstration-project root directory for this accession; child directories organize microbiome and/or reference-genome resources where present. Access: Public s3://hmpdcc/hmp1/demo/PRJNA46337/
Download Guide
— HMP
Demonstration Projects
Project directory 		PRJNA46339 demonstration project directory
Multiple data types · Project collection 		BioProject title: The Human Microbiome in Pediatric Abdominal Pain and Intestinal Inflammation. HMP demonstration-project root directory for this accession; child directories organize microbiome and/or reference-genome resources where present. Access: Public s3://hmpdcc/hmp1/demo/PRJNA46339/
Download Guide
— HMP
Demonstration Projects
Project directory 		PRJNA46315 demonstration project directory
Multiple data types · Project collection 		BioProject title: The Role of the Gut Microbiota in Ulcerative Colitis, targeted gene survey. HMP demonstration-project root directory for this accession; child directories organize microbiome and/or reference-genome resources where present. Access: Public s3://hmpdcc/hmp1/demo/PRJNA46315/
Download Guide
— HMP
Demonstration Projects
Project directory 		PRJNA50637 demonstration project directory
Multiple data types · Project collection 		BioProject title: The Role of the Gut Microbiota in Ulcerative Colitis, functional gene metagenomics. HMP demonstration-project root directory for this accession; child directories organize microbiome and/or reference-genome resources where present. Access: Public s3://hmpdcc/hmp1/demo/PRJNA50637/
Download Guide
— HMP
Demonstration Projects
Project directory 		PRJNA46333 demonstration project directory
Multiple data types · Project collection 		BioProject title: Gene-Environment Interactions at the Skin Surface. HMP demonstration-project root directory for this accession; child directories organize microbiome and/or reference-genome resources where present. Access: Public s3://hmpdcc/hmp1/demo/PRJNA46333/
Download Guide
lp-hm16str HMP
Healthy Human Subjects
Microbiome 		16S trimmed reads
16S rRNA gene sequencing · Trimmed reads 		Quality-trimmed 16S ribosomal RNA gene amplicon reads from the HMP healthy human subjects collection. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/16s/analysis/trimmed/16str_2012/
Download Guide
lp-hm16str2 HMP
Healthy Human Subjects
Microbiome 		16S trimmed reads
16S rRNA gene sequencing · Trimmed reads 		Updated quality-trimmed 16S ribosomal RNA gene amplicon reads for healthy human subjects. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/16s/analysis/trimmed/16str_2017/
Download Guide
lp-hmqcp HMP
Healthy Human Subjects
Microbiome 		QIIME community profiles
16S rRNA gene sequencing · Community profile 		Taxonomic community profiles generated with QIIME from 16S data. A community profile summarizes the microorganisms detected and their relative abundances. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/16s/analysis/community_prof/qiime_2012/
Download Guide
lp-hmmcp HMP
Healthy Human Subjects
Microbiome 		mothur community profiles
16S rRNA gene sequencing · Community profile 		Taxonomic community profiles generated with mothur from 16S data. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/16s/analysis/community_prof/mothur_2012/
Download Guide
lp-hmrdp HMP
Healthy Human Subjects
Microbiome 		RDP community profiles
16S rRNA gene sequencing · Community profile 		Taxonomic community profiles generated using the Ribosomal Database Project classifier. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/16s/analysis/community_prof/rdp_2012/
Download Guide
lp-hmr16s HMP
Healthy Human Subjects
Microbiome 		16S raw-read index
16S rRNA gene sequencing · Raw-data index 		Public directory containing the README/index information used to locate raw 16S sequence runs in the Sequence Read Archive. Access: Public directory; sequence files in SRA s3://hmpdcc/hmp1/hhs/microbiome/16s/raw/
Download Guide
— HMP
Healthy Human Subjects
Microbiome 		WMS raw-read index
Whole metagenome shotgun sequencing · Raw-data index 		Public README/index directory for whole metagenome shotgun (WMS) sequence-run accessions. Access: Public directory; sequence files in SRA s3://hmpdcc/hmp1/hhs/microbiome/wms/raw/
Download Guide
lp-hmiwgs HMP
Healthy Human Subjects
Microbiome 		WMS quality-controlled reads
Whole metagenome shotgun sequencing · Quality control 		Quality-control (QC) output for whole metagenome shotgun reads; the source also identifies this collection as hmwgsqc_v1. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/qc/qc_2012/
Download Guide
lp-hmwgsqc2 HMP
Healthy Human Subjects
Microbiome 		WMS quality-controlled reads
Whole metagenome shotgun sequencing · Quality control 		Updated quality-control output for HMP whole metagenome shotgun reads. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/qc/qc_2017/
Download Guide
lp-hmasm HMP
Healthy Human Subjects
Microbiome 		Single-sample assemblies
Whole metagenome shotgun sequencing · Assembly 		Assembly of each WMS sample into contigs and scaffolds. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/assemblies/single_sample/ssasm_2012/
Download Guide
lp-hmasm2 HMP
Healthy Human Subjects
Microbiome 		Single-sample assemblies
Whole metagenome shotgun sequencing · Assembly 		Updated single-sample WMS assemblies. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/assemblies/single_sample/ssasm_2017/
Download Guide
lp-hmbsa HMP
Healthy Human Subjects
Microbiome 		Body-site assemblies
Whole metagenome shotgun sequencing · Assembly 		Assemblies generated by pooling unassembled reads by body site. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/assemblies/bodysite_asm_2012/
Download Guide
lp-hmhasm HMP
Healthy Human Subjects
Microbiome 		Hybrid assemblies
Whole metagenome shotgun sequencing · Assembly 		Hybrid assemblies combining complementary sequencing data. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/assemblies/hybrid_asm_2012/
Download Guide
lp-hmcasm2 HMP
Healthy Human Subjects
Microbiome 		Co-assemblies
Whole metagenome shotgun sequencing · Assembly 		Co-assemblies generated across related WMS samples. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/assemblies/coasm_2017/
Download Guide
lp-hmgi HMP
Healthy Human Subjects
Microbiome 		Gene index
Whole metagenome shotgun sequencing · Annotation 		A gene index is a catalog of genes predicted from HMP metagenomic assemblies. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/annotation/gene_index/gi_2012/
Download Guide
lp-hmgi2 HMP
Healthy Human Subjects
Microbiome 		Gene index
Whole metagenome shotgun sequencing · Annotation 		Updated catalog of genes predicted from metagenomic assemblies. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/annotation/gene_index/gi_2017/
Download Guide
lp-hmhgi HMP
Healthy Human Subjects
Microbiome 		Hybrid-assembly gene index
Whole metagenome shotgun sequencing · Annotation 		Gene index predicted from hybrid assemblies. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/annotation/gene_index/gi_hyb_2012/
Download Guide
lp-hmcgi2 HMP
Healthy Human Subjects
Microbiome 		Co-assembly gene index
Whole metagenome shotgun sequencing · Annotation 		Gene index predicted from WMS co-assemblies. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/annotation/gene_index/gi_coasm_2017/
Download Guide
lp-hmgc HMP
Healthy Human Subjects
Microbiome 		Gene clusters
Whole metagenome shotgun sequencing · Annotation 		Clusters group related predicted genes to reduce redundancy and support comparative analysis. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/annotation/gene_clusters/gc_2012/
Download Guide
lp-hmgc2 HMP
Healthy Human Subjects
Microbiome 		Gene clusters
Whole metagenome shotgun sequencing · Annotation 		Updated clusters of related predicted genes. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/annotation/gene_clusters/gc_2017/
Download Guide
lp-hmcgc2 HMP
Healthy Human Subjects
Microbiome 		Co-assembly gene clusters
Whole metagenome shotgun sequencing · Annotation 		Gene clusters derived from co-assembly gene predictions. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/annotation/gene_clusters/gc_coasm_2017/
Download Guide
lp-hmgoi HMP
Healthy Human Subjects
Microbiome 		Genes of interest
Whole metagenome shotgun sequencing · Annotation 		Selected predicted genes organized for focused biological analysis. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/annotation/genes_of_int/
Download Guide
lp-hmrac2 HMP
Healthy Human Subjects
Microbiome 		Read-to-contig alignments
Whole metagenome shotgun sequencing · Alignment 		Alignments connecting WMS reads to assembled contigs. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/alignments/read2contig_2017/
Download Guide
lp-hmrarg2 HMP
Healthy Human Subjects
Microbiome 		Read-to-reference alignments
Whole metagenome shotgun sequencing · Alignment 		Alignments connecting WMS reads to reference genomes. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/alignments/read2ref_2017/
Download Guide
lp-hmcarg2 HMP
Healthy Human Subjects
Microbiome 		Contig-to-reference alignments
Whole metagenome shotgun sequencing · Alignment 		Alignments connecting assembled contigs to reference genomes. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/alignments/contig2ref_2017/
Download Guide
lp-hmccarg2 HMP
Healthy Human Subjects
Microbiome 		Co-assembly contig-to-reference alignments
Whole metagenome shotgun sequencing · Alignment 		Alignments connecting co-assembled contigs to reference genomes. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/alignments/coasm_contig2ref_2017/
Download Guide
lp-hmscp HMP
Healthy Human Subjects
Microbiome 		Reference-alignment community profiles
Whole metagenome shotgun sequencing · Community profile 		Community profiles inferred by aligning reads to microbial reference genomes. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/community_prof/refalign/
Download Guide
lp-hmsmcp HMP
Healthy Human Subjects
Microbiome 		MetaPhlAn community profiles
Whole metagenome shotgun sequencing · Community profile 		Taxonomic community profiles produced with MetaPhlAn version 1. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/community_prof/metaphlan1_2012/
Download Guide
lp-hmsmcp2 HMP
Healthy Human Subjects
Microbiome 		MetaPhlAn 2 community profiles
Whole metagenome shotgun sequencing · Community profile 		Taxonomic community profiles produced with MetaPhlAn version 2. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/community_prof/metaphlan2_2017/
Download Guide
lp-hmmrc HMP
Healthy Human Subjects
Microbiome 		HUMAnN metabolic profiles
Whole metagenome shotgun sequencing · Metabolic profile 		Metabolic profiles summarize pathways and functional potential inferred from WMS reads using HUMAnN. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/metabolic_prof/humann1_2012/
Download Guide
lp-hmmrc2 HMP
Healthy Human Subjects
Microbiome 		HUMAnN2 metabolic profiles
Whole metagenome shotgun sequencing · Metabolic profile 		Updated metabolic and pathway profiles generated with HUMAnN2. Access: Public s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/metabolic_prof/humann2_2017/
Download Guide
lp-hmrgd HMP
Reference Genomes
Reference genome 		HMP reference genome collection
Reference genomes · Collection 		Reference genome sequences and derived products for microorganisms associated with the human body. Access: Public s3://hmpdcc/hmp1/hhs/refgenome/
Download Guide
lp-hmrgd HMP
Reference Genomes
Reference genome 		Reference genome contigs
Reference genomes · Assembly 		Contiguous assembled reference-genome sequences. Access: Public s3://hmpdcc/hmp1/hhs/refgenome/assemblies/contigs/
Download Guide
lp-hmrgd HMP
Reference Genomes
Reference genome 		Reference genome scaffolds
Reference genomes · Assembly 		Scaffolded reference-genome assemblies. Access: Public s3://hmpdcc/hmp1/hhs/refgenome/assemblies/scaffolds/
Download Guide
lp-hmrgd HMP
Reference Genomes
Reference genome 		Science annotations: GenBank-formatted annotations
Reference genomes · Annotation 		GenBank-formatted annotations from the science annotations release. Access: Public s3://hmpdcc/hmp1/hhs/refgenome/annotation/science_2010/gbk/
Download Guide
lp-hmrgd HMP
Reference Genomes
Reference genome 		Science annotations: Coding DNA sequences
Reference genomes · Annotation 		Coding DNA sequences from the science annotations release. Access: Public s3://hmpdcc/hmp1/hhs/refgenome/annotation/science_2010/cds/
Download Guide
lp-hmrgd HMP
Reference Genomes
Reference genome 		Science annotations: Predicted protein sequences
Reference genomes · Annotation 		Predicted protein sequences from the science annotations release. Access: Public s3://hmpdcc/hmp1/hhs/refgenome/annotation/science_2010/pep/
Download Guide
lp-hmrgd HMP
Reference Genomes
Reference genome 		JCVI annotations: GenBank-formatted annotations
Reference genomes · Annotation 		GenBank-formatted annotations from the jcvi annotations release. Access: Public s3://hmpdcc/hmp1/hhs/refgenome/annotation/jcvi_2013/gbk/
Download Guide
lp-hmrgd HMP
Reference Genomes
Reference genome 		JCVI annotations: Coding DNA sequences
Reference genomes · Annotation 		Coding DNA sequences from the jcvi annotations release. Access: Public s3://hmpdcc/hmp1/hhs/refgenome/annotation/jcvi_2013/cds/
Download Guide
lp-hmrgd HMP
Reference Genomes
Reference genome 		JCVI annotations: Predicted protein sequences
Reference genomes · Annotation 		Predicted protein sequences from the jcvi annotations release. Access: Public s3://hmpdcc/hmp1/hhs/refgenome/annotation/jcvi_2013/pep/
Download Guide
lp-hmrgd HMP
Reference Genomes
Reference genome 		Gales annotations: Coding DNA sequences
Reference genomes · Annotation 		Coding DNA sequences from the Gales reference-genome annotation release. Access: Public s3://hmpdcc/hmp1/hhs/refgenome/annotation/gales_2018/cds/
Download Guide
lp-hmrgd HMP
Reference Genomes
Reference genome 		Gales annotations: Predicted protein sequences
Reference genomes · Annotation 		Predicted protein sequences from the Gales reference-genome annotation release. Access: Public s3://hmpdcc/hmp1/hhs/refgenome/annotation/gales_2018/pep/
Download Guide
lp-hmmda16s HMP
Reference Genomes
Reference genome 		Small-subunit marker database
16S rRNA gene sequencing · Reference database 		Reference-genome small-subunit/16S marker data used for microbiome analysis. Access: Public s3://hmpdcc/hmp1/hhs/refgenome/ssmda16s/
Download Guide
lp-hmrefg HMP
Reference Genomes
Reference genome 		Reference genome search database
Reference genomes · Search database 		Searchable 2012 reference-genome database prepared for sequence comparison. Access: Public s3://hmpdcc/hmp1/hhs/refgenome/refgenome_search_db_2012/
Download Guide
dmz-hm16str iHMP
Inflammatory Bowel Disease
Microbiome 		16S trimmed reads
16S rRNA gene sequencing · Trimmed reads 		Quality-trimmed longitudinal 16S ribosomal RNA gene amplicon reads for the IBD Multi-omics Database study. Access: Public s3://hmpdcc/ihmp/ibdmdb/microbiome/16s/analysis/trimmed/16str_2019/
Download Guide
dmz-hm16str iHMP
Inflammatory Bowel Disease
Microbiome 		16S trimmed reads
16S rRNA gene sequencing · Trimmed reads 		Updated quality-trimmed 16S amplicon reads for the IBD study. Access: Public s3://hmpdcc/ihmp/ibdmdb/microbiome/16s/analysis/trimmed/16str_2020/
Download Guide
hmqcp iHMP
Inflammatory Bowel Disease
Microbiome 		QIIME community profiles
16S rRNA gene sequencing · Community profile 		QIIME 16S community profiles for IBD. The mapping source writes the identifier as hmqcp without an lp-, dm-, or dmz- prefix. Access: Public s3://hmpdcc/ihmp/ibdmdb/microbiome/16s/analysis/community_prof/qiime_2019/
Download Guide
— iHMP
Inflammatory Bowel Disease
Microbiome 		DADA2 community profiles
16S rRNA gene sequencing · Community profile 		DADA2 amplicon-sequence-variant community profiles for IBD. Access: Public s3://hmpdcc/ihmp/ibdmdb/microbiome/16s/analysis/community_prof/dada2_2020/
Download Guide
— iHMP
Inflammatory Bowel Disease
Microbiome 		16S raw-read index
16S rRNA gene sequencing · Raw-data index 		README/index for locating raw IBD 16S sequence files. Access: Public directory; sequence files may be in SRA s3://hmpdcc/ihmp/ibdmdb/microbiome/16s/raw/
Download Guide
dmz-hmmrc iHMP
Inflammatory Bowel Disease
Microbiome 		HUMAnN2 metabolic profiles
Whole metagenome shotgun sequencing · Metabolic profile 		Longitudinal microbial pathway and metabolic profiles generated with HUMAnN2. Access: Public s3://hmpdcc/ihmp/ibdmdb/microbiome/wms/analysis/metabolic_prof/humann2_2019/
Download Guide
dm-hmscp iHMP
Inflammatory Bowel Disease
Microbiome 		MetaPhlAn community profiles
Whole metagenome shotgun sequencing · Community profile 		Taxonomic community profiles generated from IBD WMS data with MetaPhlAn. Access: Public s3://hmpdcc/ihmp/ibdmdb/microbiome/wms/analysis/community_prof/metaphlan_2019/
Download Guide
dmz-hmvir iHMP
Inflammatory Bowel Disease
Microbiome 		Virome products
Whole metagenome shotgun sequencing · Virome analysis 		Viral-community analysis products associated with the IBD WMS data. Access: Public s3://hmpdcc/ihmp/ibdmdb/microbiome/wms/analysis/virome/
Download Guide
— iHMP
Inflammatory Bowel Disease
Microbiome 		WMS raw-read index
Whole metagenome shotgun sequencing · Raw-data index 		README/index for raw IBD whole metagenome shotgun reads. Access: Public directory; sequence files may be in SRA s3://hmpdcc/ihmp/ibdmdb/microbiome/wms/raw/
Download Guide
— iHMP
Inflammatory Bowel Disease
Microbiome 		Proteome
Proteomics · Processed collection 		Microbial protein-abundance measurements. Access: Public s3://hmpdcc/ihmp/ibdmdb/microbiome/proteome/
Download Guide
— iHMP
Inflammatory Bowel Disease
Microbiome 		Metatranscriptome HUMAnN2 profiles
Metatranscriptomics · Metabolic profile 		Functional profiles generated from microbial metatranscriptome data with HUMAnN2. Access: Public s3://hmpdcc/ihmp/ibdmdb/microbiome/metatranscriptome/analysis/humann2_2019/
Download Guide
— iHMP
Inflammatory Bowel Disease
Microbiome 		Raw metatranscriptome index
Metatranscriptomics · Raw-data index 		README/index for raw microbial RNA sequencing data. Access: Public directory; repository restrictions may apply s3://hmpdcc/ihmp/ibdmdb/microbiome/metatranscriptome/raw/
Download Guide
— iHMP
Inflammatory Bowel Disease
Host 		Serology
Serology · Processed collection 		Host serological measurements. Access: Public or repository-specific s3://hmpdcc/ihmp/ibdmdb/host/serology/
Download Guide
— iHMP
Inflammatory Bowel Disease
Host 		Host transcriptome HTSeq gene counts
Transcriptomics · Gene-count analysis 		Per-sample host-transcriptome gene-count tables generated with HTSeq version 0.6.1. Access: Public or repository-specific s3://hmpdcc/ihmp/ibdmdb/host/transcriptome/analysis/htseq0.6.1/
Download Guide
dmz-hm16str iHMP
Pregnancy and Preterm Birth / MOMS-PI
Microbiome 		16S trimmed reads
16S rRNA gene sequencing · Trimmed reads 		Quality-trimmed longitudinal 16S amplicon reads for MOMS-PI (2019 release). Access: Public s3://hmpdcc/ihmp/momspi/microbiome/16s/analysis/trimmed/16str_2019/
Download Guide
dmz-hm16str iHMP
Pregnancy and Preterm Birth / MOMS-PI
Microbiome 		16S trimmed reads
16S rRNA gene sequencing · Trimmed reads 		Quality-trimmed longitudinal 16S amplicon reads for MOMS-PI (2020 release). Access: Public s3://hmpdcc/ihmp/momspi/microbiome/16s/analysis/trimmed/16str_2020/
Download Guide
— iHMP
Pregnancy and Preterm Birth / MOMS-PI
Microbiome 		QIIME community profiles
16S rRNA gene sequencing · Community profile 		QIIME taxonomic community profiles for MOMS-PI. Access: Public s3://hmpdcc/ihmp/momspi/microbiome/16s/analysis/community_prof/qiime_2019/
Download Guide
— iHMP
Pregnancy and Preterm Birth / MOMS-PI
Microbiome 		STIRRUPS community profiles
16S rRNA gene sequencing · Community profile 		Vaginal microbial community profiles generated with STIRRUPS. Access: Public s3://hmpdcc/ihmp/momspi/microbiome/16s/analysis/community_prof/stirrups_2019/
Download Guide
— iHMP
Pregnancy and Preterm Birth / MOMS-PI
Microbiome 		DADA2 community profiles
16S rRNA gene sequencing · Community profile 		DADA2 amplicon-sequence-variant community profiles. Access: Public s3://hmpdcc/ihmp/momspi/microbiome/16s/analysis/community_prof/dada2_2020/
Download Guide
— iHMP
Pregnancy and Preterm Birth / MOMS-PI
Microbiome 		16S raw-read index
16S rRNA gene sequencing · Raw-data index 		README/index for raw MOMS-PI 16S sequence files. Access: Public directory; sequence files may be in SRA s3://hmpdcc/ihmp/momspi/microbiome/16s/raw/
Download Guide
dmz-hmmrc iHMP
Pregnancy and Preterm Birth / MOMS-PI
Microbiome 		HUMAnN2 metabolic profiles
Whole metagenome shotgun sequencing · Metabolic profile 		Microbial pathway and metabolic profiles generated with HUMAnN2. Access: Public s3://hmpdcc/ihmp/momspi/microbiome/wms/analysis/metabolic_prof/humann2_2019/
Download Guide
dmz-hmscp iHMP
Pregnancy and Preterm Birth / MOMS-PI
Microbiome 		MetaPhlAn2 community profiles
Whole metagenome shotgun sequencing · Community profile 		Taxonomic profiles generated from MOMS-PI WMS data with MetaPhlAn2. Access: Public s3://hmpdcc/ihmp/momspi/microbiome/wms/analysis/community_prof/metaphlan2_2019/
Download Guide
— iHMP
Pregnancy and Preterm Birth / MOMS-PI
Microbiome 		Metatranscriptome HUMAnN2 metabolic reconstruction
Metatranscriptomics · Metabolic reconstruction 		Metatranscriptomic gene-family, pathway-abundance, and pathway-coverage outputs generated with HUMAnN2. Access: Public s3://hmpdcc/ihmp/momspi/microbiome/metatranscriptome/analysis/metabolic_recon/humann2_2019/
Download Guide
— iHMP
Pregnancy and Preterm Birth / MOMS-PI
Microbiome 		Metatranscriptome MetaPhlAn2 community profiles
Metatranscriptomics · Community profile 		Taxonomic community profiles generated from MOMS-PI metatranscriptome data with MetaPhlAn2. Access: Public s3://hmpdcc/ihmp/momspi/microbiome/metatranscriptome/analysis/community_prof/metaphlan2_2019/
Download Guide
— iHMP
Pregnancy and Preterm Birth / MOMS-PI
Host 		Host cytokines
Cytokine measurements · Processed collection 		Host cytokine measurements collected in MOMS-PI. Access: Public or repository-specific s3://hmpdcc/ihmp/momspi/host/cytokine/
Download Guide
— iHMP
Pregnancy and Preterm Birth / MOMS-PI
Mixed host/microbiome 		Mixed lipidome
Lipidomics · Processed collection 		Lipid measurements associated with combined host and microbiome analyses. Access: Public or repository-specific s3://hmpdcc/ihmp/momspi/mixed/lipidome/
Download Guide
dmz-hm16str iHMP
Type 2 Diabetes / iPOP
Microbiome 		16S trimmed reads
16S rRNA gene sequencing · Trimmed reads 		Quality-trimmed longitudinal 16S amplicon reads for the iPOP type 2 diabetes study (2019 release). Access: Public s3://hmpdcc/ihmp/t2d/microbiome/16s/analysis/trimmed/16str_2019/
Download Guide
dmz-hm16str iHMP
Type 2 Diabetes / iPOP
Microbiome 		16S trimmed reads
16S rRNA gene sequencing · Trimmed reads 		Quality-trimmed longitudinal 16S amplicon reads for the iPOP type 2 diabetes study (2020 release). Access: Public s3://hmpdcc/ihmp/t2d/microbiome/16s/analysis/trimmed/16str_2020/
Download Guide
dmz-hmqcp iHMP
Type 2 Diabetes / iPOP
Microbiome 		QIIME community profiles
16S rRNA gene sequencing · Community profile 		QIIME taxonomic community profiles for the T2D/iPOP study. Access: Public s3://hmpdcc/ihmp/t2d/microbiome/16s/analysis/community_prof/qiime_2019/
Download Guide
— iHMP
Type 2 Diabetes / iPOP
Microbiome 		DADA2 community profiles
16S rRNA gene sequencing · Community profile 		DADA2 amplicon-sequence-variant community profiles. Access: Public s3://hmpdcc/ihmp/t2d/microbiome/16s/analysis/community_prof/dada2_2020/
Download Guide
— iHMP
Type 2 Diabetes / iPOP
Microbiome 		16S raw-read index
16S rRNA gene sequencing · Raw-data index 		README/index for raw T2D/iPOP 16S sequence files. Access: Public directory; sequence files may be in SRA s3://hmpdcc/ihmp/t2d/microbiome/16s/raw/
Download Guide
— iHMP
Type 2 Diabetes / iPOP
Microbiome 		WMS quality-controlled reads
Whole metagenome shotgun sequencing · Quality control 		Quality-control output for T2D/iPOP WMS reads. Access: Public s3://hmpdcc/ihmp/t2d/microbiome/wms/analysis/qc/qc_2020/
Download Guide
— iHMP
Type 2 Diabetes / iPOP
Microbiome 		HUMAnN2 metabolic profiles
Whole metagenome shotgun sequencing · Metabolic profile 		Microbial pathway and metabolic profiles generated with HUMAnN2. Access: Public s3://hmpdcc/ihmp/t2d/microbiome/wms/analysis/metabolic_prof/humann2_2020/
Download Guide
— iHMP
Type 2 Diabetes / iPOP
Microbiome 		MetaPhlAn2 community profiles
Whole metagenome shotgun sequencing · Community profile 		Taxonomic community profiles generated with MetaPhlAn2. Access: Public s3://hmpdcc/ihmp/t2d/microbiome/wms/analysis/community_prof/metaphlan2_2020/
Download Guide
— iHMP
Type 2 Diabetes / iPOP
Microbiome 		WMS raw reads
Whole metagenome shotgun sequencing · Raw reads 		Public T2D/iPOP raw WMS directory identified in the mapping source. Access: Public s3://hmpdcc/ihmp/t2d/microbiome/wms/raw/
Download Guide
— iHMP
Type 2 Diabetes / iPOP
Microbiome 		Raw metatranscriptome index
Metatranscriptomics · Raw-data index 		Directory for raw microbial metatranscriptome data. Access: Public or repository-specific s3://hmpdcc/ihmp/t2d/microbiome/metatranscriptome/raw/
Download Guide
— iHMP
Type 2 Diabetes / iPOP
Host 		Host cytokines
Cytokine measurements · Processed collection 		Host cytokine measurements in the T2D/iPOP longitudinal study. Access: Public or repository-specific s3://hmpdcc/ihmp/t2d/host/cytokine/
Download Guide
— iHMP
Type 2 Diabetes / iPOP
Host 		Host WGS raw-data index
Whole-genome sequencing · Raw-data index 		Directory/index for host whole-genome sequencing data. Human genomic data may require controlled-access authorization. Access: Controlled or repository-restricted s3://hmpdcc/ihmp/t2d/host/wgs/raw/
Download Guide
— iHMP
Type 2 Diabetes / iPOP
Host 		Host metabolome
Metabolomics · Processed collection 		Host metabolome measurements for the T2D/iPOP study. Access: Public or repository-specific s3://hmpdcc/ihmp/t2d/host/metabolome/
Download Guide
— iHMP
Type 2 Diabetes / iPOP
Host 		Host proteome
Proteomics · Processed collection 		Host proteome measurements for the T2D/iPOP study. Access: Public or repository-specific s3://hmpdcc/ihmp/t2d/host/proteome/
Download Guide
— iHMP
Type 2 Diabetes / iPOP
Host 		Host proteome (non-PRIDE)
Proteomics · Processed collection 		Host proteome (non-PRIDE) measurements for the T2D/iPOP study. Access: Public or repository-specific s3://hmpdcc/ihmp/t2d/host/proteome_nonpride/
Download Guide
— iHMP
Type 2 Diabetes / iPOP
Host 		Raw host transcriptome index
Transcriptomics · Raw-data index 		Directory/index for raw host transcriptome sequence data. Human sequence data may require controlled-access authorization. Access: Controlled or repository-restricted s3://hmpdcc/ihmp/t2d/host/transcriptome/raw/
Download Guide

BioProjects

The four primary BioProjects are shown first. Expand each card to view the associated accessions documented for that project or study.

HMP

HMP — PRJNA43021

Human Microbiome Project

Associated BioProject accessions

Demonstration Projects

Healthy Human Subjects

Reference Genomes

Public and controlled-access data

Public HMPDACC S3 directories can be listed and downloaded without an AWS account by using the AWS CLI option --no-sign-request. Some raw human sequence data, detailed participant metadata, and other controlled records still require authorization through dbGaP or the repository named by the study. A public directory or README does not override those repository access requirements.

Continue to the Download Guide