EsViritu
EsViritu is a read mapping pipeline for detection and measurement of human and animal virus pathogens using sequencing reads from metagenomic environmental or clinical samples.
- Source code: https://github.com/cmmr/EsViritu
- Project README: https://github.com/cmmr/EsViritu/blob/main/README.md
Why use EsViritu?
This approach is sensitive, specific, and ideal for exploring virus presence/absence/diversity within and between metagenomic or clinical samples. Interactive reports make it easy to see the breadth of read coverage for each detected virus. This tool should reliably detect virus reads with 80% ANI or greater to reference genomes.
Note
The database used by Esviritu should cover all human and animal viruses in GenBank as of October 2025 (EsViritu DB v3.2.4). However, the genomes are dereplicated at 95% ANI so that only one genome from a nearly identical group is used. Please open an issue to report any omissions.
Getting started
If installed as a package, command-line entry points are available:
EsViritu --helpsummarize_esv_runs --help
Tip
Read the other pages of the documentation to understand what EsViritu does and how to interpret its outputs.
Citation
EsViritu is a sensitive and specific profiler for viral pathogen detection and genome recovery in metagenomes
Michael J. Tisza, Shelby R. Simar, Jackie K. Zorz, Sara J. Javornik Cregeen, Anthony W. Maresso
https://doi.org/10.64898/2026.09.29.755457
Your citations and GitHub Stars help keep EsViritu going!