iVirP: An integrative, efficient, and user-friendly pipeline to annotate viral contigs from raw reads of metagenome or VLP sequencing

Metagenome sequencing and virus-like particles sequencing make it possible to explore the virome in the humans and other organisms. One way to analyze the sequencing data is to assemble reads into contigs according to the overlapping regions, and then the predicted viral contigs are screened out to conduct deeper dives. iVirP (integrative virome pipeline) is a user-friendly pipeline that includes the whole process of viral contigs discovery from the quality control of raw data to the filter of high quality viral contigs. This pipeline also features a branching function that can estimate the abundance of known eukaryotic viruses in a short period, while reducing host contamination. It is suitable for the rapid diagnosis of pathogens. Throughout iVirP, many details that might affect the experience of users are optimized carefully to reduce the time spent on dealing with usage and errors. iVirP was tested on a published, high-quality VLP sequencing dataset and was able to well reproduce the conclusions of the corresponding research. The benchmark indicates that iVirP could accurately assemble viral contigs from real sequencing data. iVirP is easy to install and currently available at https://github.com/li-bw18/iVirP.