Metadata

metadata/

Genome, vOTU, host, and sample metadata tables. 6 files

uhgv_metadata.tsv Detailed information on each of the 873,994 UHGV genomes

207 MB

uhgv_extended_metadata.tsv Detailed information on a set of 212,778 additional human gut viral genomes not included in the main catalog

65 MB

votus_metadata.tsv Detailed information on each of the 168,536 vOTUs

51 MB

votus_metadata_extra.tsv Additional information on each vOTU

128 MB

host_metadata.tsv Information for prokaryotic genomes (taxonomy, completeness, contamination, N50)

131 MB

source_biosample_metadata.tsv Information for the samples from which virus genomes were obtained

5.3 MB

Genome and protein catalogs

genome_catalogs/

Genome and protein FASTA catalogs of all UHGV genomes, vOTU representatives, and host genomes. 16 files

uhgv_full.fna.gz Genomic sequences of all genomes ≥10kb or ≥50% completeness

6.5 GB

uhgv_full.faa.gz Protein sequences of all genomes ≥10kb or ≥50% completeness

5.6 GB

uhgv_mq_plus.fna.gz Genomic sequences of all genomes with ≥50% completeness

5.1 GB

uhgv_mq_plus.faa.gz Protein sequences of all genomes with ≥50% completeness

3.8 GB

uhgv_hq_plus.fna.gz Genomic sequences of all genomes with ≥90% completeness

3.0 GB

uhgv_hq_plus.faa.gz Protein sequences of all genomes with ≥90% completeness

2.2 GB

uhgv_extended.fna.gz Genomic sequences of additional human gut viral genomes from VIRE that are not included in the main catalog

1.9 GB

uhgv_extended.faa.gz Protein sequences of additional human gut viral genomes from VIRE that are not included in the main catalog

1.1 GB

votus_full.fna.gz Genomic sequences of vOTU representatives ≥10kb or ≥50% completeness

1.3 GB

votus_full.faa.gz Protein sequences of vOTU representatives ≥10kb or ≥50% completeness

1.0 GB

votus_mq_plus.fna.gz Genomic sequences of vOTU representatives with ≥50% completeness

MQ+ 1.0 GB

votus_mq_plus.faa.gz Protein sequences of vOTU representatives with ≥50% completeness

MQ+ 796 MB

votus_hq_plus.fna.gz Genomic sequences of vOTU representatives with ≥90% completeness

MQ+ 701 MB

votus_hq_plus.faa.gz Protein sequences of vOTU representatives with ≥90% completeness

MQ+ 522 MB

host_genomes_full.tar.zst Genomic sequences of gut prokaryotes

53 GB

host_genomes_otus.tar.zst Genomic sequences of gut prokaryote OTU representatives

3.5 GB

Phylogeny

phylogeny/

Reference tree files for viral phylogenetic analysis. 1 files

caudoviricetes_tree.nwk.gz Phylogenetic tree of Caudoviricetes genomes

3.4 MB

Protein clusters

protein_clusters/

Cluster membership, consensus taxonomy, and multiple sequence alignments. 3 files

cluster_membership.tsv.gz Cluster membership of all UHGV proteins

217 MB

cluster_taxonomy.tsv.gz Consensus taxonomy (both UHGV and ICTV) for each protein cluster

60 MB

MSAs.tar.gz Multiple sequence alignments of protein clusters with ≥15 members

1.3 GB

Structures

structures/

Predicted protein structures and structure-domain annotations. 3 files

PDB.tar.gz PDB files of UHGV predicted protein structures

1.5 GB

PDB_references.tar.gz PDB files of predicted protein structures of COG, HAMAP, NCBIfam, and Pfam entries

1.4 GB

domains.tsv Domain segmentation of UHGV protein structures

2.6 MB

Annotations

annotations/

Functional annotations and mobile-element features for MQ+ vOTU representatives. 4 files

protein_annotations.tsv.gz Functional annotations for proteins encoded by MQ+ vOTU representatives

MQ+ 329 MB

structure_annotations.tsv.gz Structure-based annotations for protein clusters with predicted structures

MQ+ 1.8 MB

tRNAs.tsv.gz tRNAs predicted in MQ+ vOTU representatives

MQ+ 1.4 MB

DGRs.tsv.gz Diversity-generating retroelements predicted in MQ+ vOTU representatives

MQ+ 143 KB

vOTU representatives

votu_reps/

Per-genome files for MQ+ vOTU representative folders. 6 files

votu_reps_list.txt List of the paths to each MQ+ vOTU representative folder

MQ+ 2.2 MB

UHGV-*/UHGV-*/ Example path: UHGV-081/UHGV-0814053/

genome_id.fna DNA sequence FASTA file of the genome assembly of the vOTU representative

MQ+

genome_id.faa Protein sequence FASTA file of the vOTU representative

MQ+

genome_id.gff Genome GFF file with various sequence annotations

MQ+

genome_id_emapper.tsv eggNOG-mapper annotations for proteins

MQ+

genome_id_annotations.tsv Protein annotations from diverse reference databases (Pfam, UniRef90, NCBIfam, etc.)

MQ+

* : path wildcard genome_id : genome identifier

Host prediction

host_predictions/

Host genome metadata and host predictions for MQ+ vOTU representatives. 5 files

crispr_spacers.fna.gz 5,271,034 CRISPR spacers extracted from UHGG, GenBank, and Hadza prokaryotic genomes

MQ+ 69 MB

host_genomes_info.tsv GTDB r207 taxonomy for genomes from the UHGG, NCBI, and Hadza genomes

MQ+ 128 MB

host_assignment_crispr.tsv Detailed information for host prediction with CRISPR spacers

MQ+ 311 MB

host_assignment_kmers.tsv Detailed information for host prediction with PHIST k-mer matching

MQ+ 372 MB

host_assignment_crispr_extended.tsv Detailed information for host prediction with CRISPR spacers for additional vOTUs not included in the main catalog

MQ+ 207 MB

Read mapping

read_mapping/

Relative abundance, coverage, and sample metadata from metagenome and virome read mapping. 7 files

relative_abundance.tsv Relative abundances of viruses and bacteria across bulk genomes and viromes

MQ+ 50 MB

metagenomes_coverm.tsv.gz CoverM mapping statistics for viruses and bacteria across bulk metagenomes

MQ+ 2.7 GB

viromes_coverm.tsv.gz CoverM mapping statistics for viruses and bacteria across viral-enriched metagenomes

MQ+ 125 MB

sample_alpha_diversity.tsv Alpha diversity metrics computed for the prokaryotic and viral components of each sample

MQ+ 535 KB

sample_metadata.tsv Human sample metadata (study, country, lifestyle, age, gender, BMI, etc.)

MQ+ 584 KB

fastq_summary.tsv Information on sequencing reads (SRA accession, read count, ViromeQC enrichment, etc.)

MQ+ 382 KB

study_metadata.tsv Information on individual studies

MQ+ 16 KB

Microdiversity

microdiversity/

Variant and codon-level diversity summaries from read mapping. 2 files

SNVs.tsv.zst Single nucleotide variants identified through read mapping

MQ+ 118 MB

codon_pN_pS.tsv.zst Polymorphic codons and their synonymous/nonsynonymous substitution potentials (pS and pN)

MQ+ 121 MB