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

Niema Moshiri

VIRULIGN is another reference-guided MSA tool designed for viral genomes (Libin et al ., 2019) . While VIRULIGN also aims to support MSA of large sequence datasets, its primary objective is to produce codon-correct alignments, whereas ViralMSA's objective is to produce alignments for use in transmission clustering as fast as possible. Thus, while ViralMSA is not guaranteed to yield codon-aware alignments, it is orders of magnitude faster than VIRULIGN, which is critical for rapidly-growing epidemics. Further, VIRULIGN is codon-aware, making it appropriate for coding regions, whereas ViralMSA is appropriate for the alignment of whole viral genomes. Lastly, VIRULIGN requires a thorough annotation of the reference genome, which may be difficult to obtain (especially towards the beginning of a novel outbreak) and does not provide the user to easily utilize different reference genomes for different viral strains. ViralMSA, on the other . CC-BY 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.20.052068 doi: bioRxiv preprint N. Moshiri hand, only requires the reference genome assembly's GenBank accession number and can build any required index files on-the-fly