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Published January 28, 2026 | Version v1
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_manual_check_100 Genomad, CheckV, and DRAMv metadata for 100 randomly selected vOTUs, along with manual classification (first column) https://github.com/jamesriddellv/Grantham_Bioreactor/blob/main/01-build-vOTU-database/scripts/08-get_vOTU_metadata_and_filter.py
3_filtered_out_vOTUs Contigs flagged as vOTUs by Genomad, but removed based on lack of viral annotations and enrichment of host and transposon annotations https://github.com/jamesriddellv/Grantham_Bioreactor/blob/main/01-build-vOTU-database/scripts/08-get_vOTU_metadata_and_filter.py
4_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
5_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
6_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
7_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
8_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
9_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-and-ISA.R

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