ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes

BioRxiv : the Preprint Server for Biology
Niema Moshiri

Abstract

Motivation: In molecular epidemiology, the identification of clusters of transmissions typically requires the alignment of viral genomic sequence data. However, existing methods of multiple sequence alignment scale poorly with respect to the number of sequences. Results: ViralMSA is a user-friendly reference-guided multiple sequence alignment tool that was built to enable the alignment of ultra-large viral genome datasets. It scales linearly with the number of sequences, and it is able to align tens of thousands of full viral genomes in seconds. Availability: ViralMSA is freely available at https://github.com/niemasd/ViralMSA as an open-source software project.

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