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

Niema Moshiri

Real-time or near real-time surveillance of the spread of a pathogen can provide actionable information for public health response (Poon et al ., 2016) . Though there is currently no consensus in the world of molecular epidemiology regarding a formal definition of what exactly constitutes a "transmission cluster" (Novitsky et al ., 2017) , all current methods of inferring transmission clusters require a multiple sequence alignment (MSA) of the viral genomes: distance-based methods of transmission clustering require knowledge of homology for accurate distance measurement (Pond et al ., 2018) , and phylogenetic methods of transmission clustering require the MSA as a precursor to phylogenetic inference (Balaban et al ., 2019; Rose et al ., 2017; Ragonnet-Cronin et al ., 2013; Prosperi et al ., 2011) .