MultiVirusConsensus: An accurate and efficient open-source pipeline for identification and consensus sequence generation of multiple viruses from mixed samples
Published in Bioinformatics Advances, 2026
Recommended citation: Moshiri N (2026). "MultiVirusConsensus: An accurate and efficient open-source pipeline for identification and consensus sequence generation of multiple viruses from mixed samples." Bioinformatics Advances. In Press. Preprint doi:10.64898/2026.03.24.26349218
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