Multi disease bacterial 16S and viral metagenomics collection

Processed bacterial and viral metagenomic data for three published gut disease cohorts: inflammatory bowel disease (IBD; Norman et al. 2015, PRJEB7772), colorectal cancer (CRC; Hannigan et al. 2018, PRJNA389927), and graft-versus-host disease (GvHD; Thiele Orberg et al. 2024, PRJEB53547). Each cohort provides paired outputs from both modalities, derived from the original authors' raw sequencing reads: Bacterial (16S rRNA amplicon) — ASV inference with DADA2 v1.34.0: ASV sequences, sample × ASV abundance tables, per-ASV taxonomy assigned against SILVA 138.1 (including resolved NCBI taxids), genus-aggregated abundances, and ready-to-use phyloseq objects. Viral (metagenomics) — viral contig catalogues and contig × sample abundance matrices from ViroProfiler v0.2.5, followed by hierarchical vOTU clustering with VirNest in two variants (single-tree and multigraph), annotated against ViralRefSeq v211. vConTACT2 outputs are included as an independent cross-validation of the clustering. All processing parameters are documented in full in the accompanying README and pipeline_parameters.md, so the data can be regenerated end-to-end from the public raw reads. This is Record 1 in the series. Record 2 provides harmonized taxonomy, protein collections, and protein-cluster matrices built on these outputs. Licensed CC-BY-4.0. Please cite the original cohort studies alongside this dataset.