Code and data for: Benchmarking Seven Metagenomics Pipelines for Viral Detection Using Simulated Short- and Long-Read Wastewater Data

Code, simulation design tables, raw pipeline outputs and derived results supporting a benchmark of seven metagenomic pipelines (nf-core/taxprofiler, nf-core/taxtriage, nf-core/mag, KrakenMetaReads-nf, GOTTCHA2, CLARK, sourmash) for viral detection on simulated Illumina and PacBio HiFi wastewater data, scored against a 151-member non-phage viral ground truth. Unzip all archives into one directory to rebuild the repository layout (code/, data/, docs/); verify the downloads with MD5SUMS.txt. Reference genomes and simulated FASTQ files are not included (see README.md). Source code is also available at https://github.com/pengsihua2023/wastewater-virome-pipeline-benchmark. Version v4: the supplementary tables (Supplementary_Tables_coverage.xlsx) are renumbered S1-S14 in order of first citation in the paper; the manually added public-health entries are reported under their actual names, with taxids 37108 and 12110 identified as Meleagrid herpesvirus 1 and foot-and-mouth disease virus O and excluded from the sentinel set (11 sentinel viruses); the README records the ccs and PBSIM3 versions used for the PacBio datasets. Version v5: the PacBio generation script (code/simulation/simulate_pacbio.py) and the figures of the paper (data/analysis_708/figures_paper/) are included; the statistical-analysis note and the analysis summary describe the current datasets and results; the scripts and derived tables that listed the sentinel set now report taxids 37108 and 12110 under their actual names and count 11 sentinel viruses; notes on the first version of the simulated datasets are marked as historical.