{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Ciccolella S"],"funding":["H2020 Marie Sklodowska-Curie Actions","Università degli Studi di Milano-Bicocca"],"pagination":["625"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9017741"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["22(Suppl 15)"],"pubmed_abstract":["<h4>Background</h4>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.<h4>Results</h4>We present MALVIRUS, an easy-to-install and easy-to-use application that assists users in multiple tasks required for the analysis of a viral population, such as the SARS-CoV-2. MALVIRUS allows to: (1) construct a variant catalog consisting in a set of variations (SNPs/indels) from the population sequences, (2) efficiently genotype and annotate variants of the catalog supported by a read sample, and (3) when the considered viral species is the SARS-CoV-2, assign the input sample to the most likely Pango lineages using the genotyped variations.<h4>Conclusions</h4>Tests on Illumina and Nanopore samples proved the efficiency and the effectiveness of MALVIRUS in analyzing SARS-CoV-2 strain samples with respect to publicly available data provided by NCBI and the more complete dataset provided by GISAID. A comparison with state-of-the-art tools showed that MALVIRUS is always more precise and often have a better recall."],"journal":["BMC bioinformatics"],"pubmed_title":["MALVIRUS: an integrated application for viral variant analysis."],"pmcid":["PMC9017741"],"funding_grant_id":["2019-ATE-0533","872539"],"pubmed_authors":["Della Vedova G","Pirola Y","Ciccolella S","Bonizzoni P","Denti L","Previtali M"],"additional_accession":[]},"is_claimable":false,"name":"MALVIRUS: an integrated application for viral variant analysis.","description":"<h4>Background</h4>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.<h4>Results</h4>We present MALVIRUS, an easy-to-install and easy-to-use application that assists users in multiple tasks required for the analysis of a viral population, such as the SARS-CoV-2. MALVIRUS allows to: (1) construct a variant catalog consisting in a set of variations (SNPs/indels) from the population sequences, (2) efficiently genotype and annotate variants of the catalog supported by a read sample, and (3) when the considered viral species is the SARS-CoV-2, assign the input sample to the most likely Pango lineages using the genotyped variations.<h4>Conclusions</h4>Tests on Illumina and Nanopore samples proved the efficiency and the effectiveness of MALVIRUS in analyzing SARS-CoV-2 strain samples with respect to publicly available data provided by NCBI and the more complete dataset provided by GISAID. A comparison with state-of-the-art tools showed that MALVIRUS is always more precise and often have a better recall.","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 Apr","modification":"2026-04-08T10:00:37.065Z","creation":"2024-11-13T17:42:51.363Z"},"accession":"S-EPMC9017741","cross_references":{"pubmed":["35439933"],"doi":["10.1186/s12859-022-04668-0"]}}