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.

中文翻译：

---

MALVIRUS：用于病毒变异调用的集成Web应用程序

如要在COVID-19大流行期间所证明的那样，为了能够追踪病毒株在全球范围内的传播，能够每天从多个病毒株产生的越来越多的测序数据中有效地调用变体至关重要。我们介绍MALVIRUS，这是一种易于安装且易于使用的Web应用程序，可帮助用户完成两项任务：（1）从种群序列计算包含一组种群SNP位点的变体目录，以及（2）有效地调用阅读样本中目录的变体。在Illumina和Nanopore样品上进行的测试证明了MALVIRUS在SARS-CoV-2菌株样品基因分型方面相对于GISAID数据的效率和有效性。