Luecking et al 2026 - Supplementary Information - "A multilayered network reveals the centrality of newly discovered Nucleocytoviricota in wastewater treatment plant communities"

Supplementary Material for the publication "A multilayered network reveals the centrality of newly discovered Nucleocytoviricota in wastewater treatment plant communities". Link to publication: Submitted / pending. Link to accompanying github interactive homepage: https://dluecking.github.io/wwtp_linking_homepage/ Data is organized into four folders: clusters - Html and pdf files of cluster plots that depict the network surrounding NVC and VPH/PLV contigs. Additionally, raw data for the creation of the network is provided. clusters/ # Network cluster visualizations + raw data├── centrality_analysis # Centrality analysis outputs├── html # Interactive HTML cluster plots│ └── lib # JS/CSS libraries required by HTML plots├── network_raw_data # Raw data used to generate network layers└── pdf # Static PDF versions of cluster plots genomes - For NCVs and PLVs/VPHs contigs (fasta), proteins (faa) and annotation files (csv) are provided. genomes/ # Genome, protein, and annotation files├── ncv # Nucleocytoviricota (NCV) genome data│ ├── annotation # Annotation tables for NCV contigs│ ├── contigs # NCV contig FASTA files│ ├── graph_files # Graph data used in network analyses│ ├── graph_plots # Plots generated from graph analyses│ └── proteins # NCV protein FASTA files (.faa)└── vph_plv # Virophage / PLV genome data ├── annotations # Annotation tables for VPH/PLV contigs ├── contigs # VPH/PLV contig FASTA files └── proteins # VPH/PLV protein FASTA files phylogenetics - For NCVs nuphylo output is provided. This results in 9 subdirectories (GVOGm0013, GVOGm0022, GVOGm0023, GVOGm0054, GVOGm0172, GVOGm0461, GVOGm0760, GVOGm0890), each containign input sequences (allseqs.faa), an alignment (allseqs.aln), a trimmed alignment (allseqs.trimmed.aln) and a tree in newick format (allseqs.aln). Additionally a combined astral tree, combining all 9 previously mentioned trees. For VPHs/PLVs files for the creation of a final tree with iqtree2 as well as all output files are provided. phylogenetics/ # Phylogenetic inputs and outputs├── ncv # NCV phylogenetic datasets (9 marker genes)│ ├── input_proteins # NCV proteins used as input for NuPhylo│ └── nuphylo_output # NuPhylo results (alignments, trees, ASTRAL)└── vph_plv # VPH/PLV phylogenetic data scripts - Contains custom scripts used in this study scripts/ ├── diamond_assign_classfication.sh # Script to assign taxonomy to input contig, by majority blastp against nr.└── pysam_filter_and_extract_overhangs.py # Script to extract overhanging reads from bam file.