Diversity and Distinctive Characteristics of the Global RNA Virome in Urban Environments

globalRNAvirus ├──all_viruses_genomad # Standard outputs of geNomad for all contigs. ├──checkCRISPRspacer # TSV files of blastn CRISPR spacer search. │ ├──match_img # IMG/VR │ └──match_uhgg # UHGG ├──checkV # Standard outputs of CheckV for RvOTUs. ├──phylogenetic tree # NWK trees and corresponding afa(multiple sequence alignment) files. │ ├──unknown_clu25(Fig.2A) │ ├──Duplornaviricota(Fig.2D) │ └──pathogen families(Fig.6E) ├──RCR95 │ ├──2_3_motif_loc_sorted_sim.tsv # Result of motif A-D detection. │ ├──besthit.csv # Tblastn best-hits from ICTV-VMR references. │ ├──RCR95_cluster.csv │ ├──RCR95_contigs.fna │ ├──RCR95_core.faa # Trimmed protein sequences of core RdRPs. │ └──unknown_clu25_taxonomy_annotation.csv # Phylogenetic tree-based taxonomic annotation for 25 phylum-level-unclassified clusters. (Fig.2A) ├──RvOTU_lineage.csv # Taxonomic annotation for RvOTUs. A subset of [./all_viruses_genomad/all_viral_contigs_genomad_taxonomy.tsv]. └──RvOTUs.fna