Data-Driven Virus Discovery with Virushunter and Virusgatherer
Chuprikova L, Chong L, Ruff S, Seitz S, Lauber C
Erschienen in
Nar Genomics and Bioinformatics: Volume 8, Issue 4, Page lqag120
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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