VirMake: a flexible and user-friendly pipeline for viral taxonomic and functional characterisation from shotgun metagenomic sequencing data

The paper describes VirMake, a flexible, scalable bioinformatic pipeline for viral taxonomic and functional characterization from shotgun metagenomic sequencing data. The authors developed an end-to-end workflow that performs viral sequence identification, metagenomic assembly, and taxonomic/functional annotation, with a modular design that lets users integrate viral analysis at different stages. They demonstrate VirMake on three metagenomic datasets (up to 2.9 Tbp) from human gut and water, using different sample preparation approaches including VLP enrichment versus bulk DNA extraction, finding that viral genome richness, taxonomy, and annotation integration vary by environment and laboratory protocol. The paper’s limitation is that the showcased results are confined to these particular datasets and environments rather than broadly covering all possible sampling and preparation conditions. The paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.

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