MultiVirusConsensus: an accurate and efficient open-source pipeline for identification and consensus sequence generation of multiple viruses from mixed samples.

MOTIVATION: Viral surveillance from mixed samples (e.g. wastewater) has become critical in public health efforts to track and contain pathogens. However, existing open-source bioinformatics tools for viral consensus sequence generation are optimized for individual viruses (rather than multiple potential viruses of interest). RESULTS: MultiVirusConsensus (MVC) is an accurate and efficient open-source pipeline for identification and consensus sequence generation of multiple viruses from mixed samples. It utilizes the memory-efficient ViralConsensus tool to simultaneously perform consensus sequence calling on all viruses of interest (1) completely in parallel, and (2) by piping datastreams between tools without writing/reading intermediate files (thus eliminating slowdowns related to slow disk accesses). AVAILABILITY: MultiVirusConsensus (MVC) is freely available as an open-source software project at: https://github.com/niemasd/MultiVirusConsensus.