Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery.

ABSTRACT: We present Microseek, a pipeline for virus identification and discovery based on RVDB-prot, a comprehensive, curated and regularly updated database of viral proteins. Microseek analyzes metagenomic Next Generation Sequencing (mNGS) raw data by performing quality steps, de novo assembly, and by scoring the Lowest Common Ancestor (LCA) from translated reads and contigs. Microseek runs on a local computer. The outcome of the pipeline is displayed through a user-friendly and dynamic graphical interface. Based on two representative mNGS datasets derived from human tissue and plasma specimens, we illustrate how Microseek works, and we report its performances. In silico spikes of known viral sequences, but also spikes of fake Neopneumovirus viral sequences generated with variable evolution

SUBMITTER: Perot P 

PROVIDER: S-EPMC9500916 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature