MALVIRUS: an integrated web application for viral variant calling

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: O_LIcomputing a variant catalog consisting in a set of population SNP loci from the population sequences and C_LIO_LIefficiently calling variants of the catalog from a read sample. C_LI 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.