Supplementary Data from Riddell V et al.

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