Abstract
Being able to efficiently call variants from the increasing amount of sequencing data daily produced from multiple viral strains is of the utmost importance, as demonstrated during the COVID-19 pandemic, in order to track the spread of the viral strains across the globe.
We present MALVIRUS, an easy-to-install and easy-to-use web application that assists users in two tasks:
computing a variant catalog consisting in a set of population SNP loci from the population sequences and
efficiently calling variants of the catalog from a read sample.
Tests on Illumina and Nanopore samples prove the efficiency and the effectiveness of MALVIRUS in genotyping SARS-CoV-2 strain samples with respect to GISAID data.
Competing Interest Statement
The authors have declared no competing interest.
