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

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ID: 327534
2026
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Abstract
Abstract 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
Reference Key
openalex_W7142887229 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Niema Moshiri
Journal Bioinformatics advances
Year 2026
DOI
10.1093/bioadv/vbag256
URL
https://academic.oup.com/bioinformaticsadvances/advance-article-pdf/doi/10.1093/bioadv/vbag256/70934952/vbag256.pdf
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