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

## Data Organization The data is organized into four main folders: ### clusters/HTML and PDF files of cluster plots depicting the network surrounding NCV 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 across 9 subdirectories (`GVOGm0013`, `GVOGm0022`, `GVOGm0023`, `GVOGm0054`, `GVOGm0172`, `GVOGm0461`, `GVOGm0760`, `GVOGm0890`), each containing:- input sequences (`allseqs.faa`)- an alignment (`allseqs.aln`)- a trimmed alignment (`allseqs.trimmed.aln`)- a tree in newick format (`allseqs.tree`) Additionally, the concatenated alignment as well as an IQ-TREE2 claculated treefile is provided.For VPHs/PLVs, input proteins, trimmed alignment and resulting treefiles 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.```├── diamond_assign_classfication.sh # Assigns taxonomy to input contigs via majority blastp against nr└── pysam_filter_and_extract_overhangs.py # Extracts overhanging reads from BAM files```