MALVIRUS: an integrated web application for viral variant calling

Motivation: 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. Results: We present MALVIRUS, an easy-to-install and easy-to-use web application that assists users in (1) computing a variant catalog consisting in a set of population SNP loci from the population sequences and (2) efficiently calling variants of the catalog that are in the sample. Tests on Illumina and Nanopore samples prove the efficiency and the effectiveness of MALVIRUS in genotyping a SARS-CoV-2 strain sample with respect to GISAID data. Availability: MALVIRUS is freely available at https://algolab.github.io/MALVIRUS/.