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bioRxiv · 10.64898/2026.01.26.701714

Data-Driven Virus Discovery with Virushunter and Virusgatherer

Chuprikova, L.·Chong, L. C.·Ruff, S.·Seitz, S.·Lauber, C.
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Abstract

We present Virushunter and Virusgatherer, a bipartite computational workflow for discovering viral genomes from unprocessed next-generation sequencing data. Virushunter conducts a profile Hidden Markov Model-based sequence homology search for viral hallmark protein-coding sequence reads to construct microcontigs, which are used as seeds for targeted viral genome assembly by Virusgatherer. We showcase the application of Virushunter and Virusgatherer through an RNA virus-wide screen in 3348 bat transcriptome sequencing experiments from the Sequence Read Archive. Many of the discovered viruses are likely prototypes of new putative virus species, including a novel alphacoronavirus identified in a South American velvety free-tailed bat and a novel rhabdovirus in a European barbastelle bat. The tools are implemented as a reproducible Snakemake pipeline, which is available at https://github.com/lauberlab/VirusHunterGatherer.

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Chuprikova, L., Chong, L. C., Ruff, S., Seitz, S., Lauber, C.. 2026-01-28. Data-Driven Virus Discovery with Virushunter and Virusgatherer. https://doi.org/10.64898/2026.01.26.701714

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