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 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 via bash process substitution 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 is freely available as an open-source software project at: https://github.com/niemasd/MultiVirusConsensus Contact niema@ucsd.edu