Accurate metagenomic profiling && Fast large-scale sequence/genome searching
A listing of software, tools and databases useful for virome analysis
Discover and annotate the virome
hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)
Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
ViromeQC is a computational tool to benchmark and quantify non-viral contamination in VLP-enrihed viromes. ViromeQC provides an enrichment score for each virome. The score is calculated with respect to the expected prokaryotic markers abundances in reference metagenomes
ViBE: a hierarchical BERT model to identify viruses using metagenome sequencing data
The Soil Virome Analysis Pipeline (SOVAP) is designed to process, analyze, and annotate viromics and metagenomics data using cutting-edge tools, providing valuable insights into the virome and microbial communities found in complex environments, such as soil ecosystems.
Gut-metagenome multi-kingdom analysis platform: 183-script + Snakemake pipeline, agent-driven mining loop, MCP visualization — VibeCoding-ready
The Metagenome-Assembled Genome Inventory for Children (MAGIC)
discover-virome: identify and quantify viruses from metagenomic assemblies
quantify-virome: identify and quantify viruses from metagenomic shotgun sequences
A novel ML-based binary classifier to tell viral and non-viral long reads apart in metagenomic samples.
microbialites stromatolites metagenomes metagenomics denovo-assembly
Viral contig analysis (hecatomb-lite)
Mosquito Virome Emergence Framework — companion code for Hoyos-López (2026), Briefings in Bioinformatics
High-performance virome-specific QC platform for the Human Virome Program
A viral genomics workflow package for read classification, reference-guided consensus, amplicon sequencing, and virome discovery.
Antimicrobial peptide mining in the Arctic permafrost virome, with a 6-part validation that stress-tests its own results
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