ArticleBMC bioinformatics2022
MALVIRUS: an integrated application for viral variant analysis.
Article in BMC bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
6 citing papers in PubMed, 6 citations in OpenAlex.
- Spatiotemporal Dynamics of SARS-CoV-2 Variants During the First Year of the Pandemic Highlight the Earlier Emergence of the Zeta Variant of Interest in Brazil.Pathogens (Basel, Switzerland) · 2024Article
- Nanopore sequencing technology and its applications.MedComm · 2023Review
- Increased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil.Nature communications · 2023Article
- Increased interregional virus exchange and nucleotide diversity outline the expansion of the chikungunya virus ECSA lineage in Brazil.medRxiv : the preprint server for health sciences · 2023Article
- Rapid genotyping of targeted viral samples using Illumina short-read sequencing data.PloS one · 2022Article
- Genomic characterization of SARS-CoV-2 isolates from patients in Turkey reveals the presence of novel mutations in spike and nsp12 proteins.Journal of medical virology · 2021Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundBeing 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.
resultsWe 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.
conclusionsTests 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.