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MALVIRUS: an integrated web application for viral variant calling

View ORCID ProfileSimone Ciccolella, View ORCID ProfileLuca Denti, View ORCID ProfilePaola Bonizzoni, View ORCID ProfileGianluca Della Vedova, View ORCID ProfileYuri Pirola, View ORCID ProfileMarco Previtali
doi: https://doi.org/10.1101/2020.05.05.076992
Simone Ciccolella
1Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
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Luca Denti
1Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
2Institut Pasteur, C3BI - USR 3756, 25-28 rue du Docteur Roux, Paris, France
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Paola Bonizzoni
1Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
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Gianluca Della Vedova
1Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
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Yuri Pirola
1Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
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  • For correspondence: yuri.pirola@unimib.it
Marco Previtali
1Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
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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:

  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 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.

Footnotes

  • ↵† Joint First Authors

  • ↵* Joint Last Authors

  • https://algolab.github.io/MALVIRUS/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 20, 2020.
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MALVIRUS: an integrated web application for viral variant calling
Simone Ciccolella, Luca Denti, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali
bioRxiv 2020.05.05.076992; doi: https://doi.org/10.1101/2020.05.05.076992
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MALVIRUS: an integrated web application for viral variant calling
Simone Ciccolella, Luca Denti, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali
bioRxiv 2020.05.05.076992; doi: https://doi.org/10.1101/2020.05.05.076992

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