Published June 6, 2026 | Version v2
Dataset Open

Supplementary Data from Riddell V et al.

Authors/Creators

  • 1. ROR icon The Ohio State University

Description

Tab Description Code used to generate
1_sequencing_accessions Metagenome and metatranscriptomes, accession numbers, and number of reads NA
2_vOTU_metadata Genomad, CheckV, and DRAMv annotations for each vOTU that passed manual filtering  https://github.com/jamesriddellv/Grantham_Bioreactor/blob/main/01-build-vOTU-database/scripts/08-get_vOTU_metadata_and_filter.py
3_post_hoc_power Power analysis of alpha diversity statistical analysis https://github.com/jamesriddellv/Grantham_Bioreactor/blob/main/02-get-relative-abundance/scripts/07-alpha_diversity.py
4_vOTU_MAG_predictions_no_cutoff iPHoP MAG-level predictions for all 9,092 vOTUs that passed manual check. Activity status of vOTUs and MAGs are listed in the last few columns https://github.com/jamesriddellv/Grantham_Bioreactor/blob/main/03-predict-hosts/scripts/06-host-prediction-EDA.py
5_cytoscape_node_metadata Metadata to reconstruct the vOTU-MAG network plot https://github.com/jamesriddellv/Grantham_Bioreactor/blob/main/03-predict-hosts/scripts/06-host-prediction-EDA.py
6_viral_taxonomy vConTACT3 viral taxonomy for all manually filtered vOTUs https://github.com/jamesriddellv/Grantham_Bioreactor/blob/main/04-viral-taxonomy/scripts/run-vcontact3.sh
7_amg_summary_QC_with_host_pred Genes flagged as AMGs from active vOTUs https://github.com/jamesriddellv/Grantham_Bioreactor/blob/main/01-build-vOTU-database/scripts/11-get_AMGs_from_active_vOTUs.py
8_indicator_vOTUs vOTUs considered indicators for at least one combination of sample clusters based on Indicator Species Analysis https://github.com/jamesriddellv/Grantham_Bioreactor/blob/main/02-get-relative-abundance/scripts/07-beta-diversity-02-D-upset.R
9_c591846_iPHoP_Detailed_Output iPHoP BLAST scores for contig_591846 predicted to infect JAGFXR01 MAGs https://github.com/jamesriddellv/Grantham_Bioreactor/blob/main/03-predict-hosts/scripts/05-run-iphop-on-custom-database.sh

Files

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Additional details

Dates

Submitted
2026-05-17