Virushunter 与 Virusgatherer 发布从原始测序数据发现病毒基因组的流程
Data-Driven Virus Discovery with Virushunter and Virusgatherer
Virushunter 与 Virusgatherer 是一套从原始下一代测序数据中发现病毒基因组的双模块计算流程：Virushunter 基于 profile Hidden Markov Model 对病毒标志蛋白编码序列 reads 做同源搜索并构建 microcontigs，再作为种子交由 Virusgatherer 进行靶向病毒基因组组装。
来源：NAR Genomics and Bioinformatics · doi.org
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.