Background: 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 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. Conclusions: 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.

Ciccolella, S., Denti, L., Bonizzoni, P., Della Vedova, G., Pirola, Y., Previtali, M. (2022). MALVIRUS: an integrated application for viral variant analysis. BMC BIOINFORMATICS, 22(S15) [10.1186/s12859-022-04668-0].

MALVIRUS: an integrated application for viral variant analysis

Ciccolella S.
Co-primo
;
Denti L.
Co-primo
;
Bonizzoni P.;Della Vedova G.;Pirola Y.
Co-ultimo
;
Previtali M.
Co-ultimo
2022

Abstract

Background: 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 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. Conclusions: 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.
Articolo in rivista - Articolo scientifico
Genotyping; Lineage classification; SARS-CoV-2; Sequence analysis; Virus;
English
Ciccolella, S., Denti, L., Bonizzoni, P., Della Vedova, G., Pirola, Y., Previtali, M. (2022). MALVIRUS: an integrated application for viral variant analysis. BMC BIOINFORMATICS, 22(S15) [10.1186/s12859-022-04668-0].
Ciccolella, S; Denti, L; Bonizzoni, P; Della Vedova, G; Pirola, Y; Previtali, M
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/370398
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