MALVIRUS: an integrated application for viral variant analysis.
MALVIRUS: an integrated application for viral variant analysis.
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DOI：
10.1186/s12859-022-04668-0
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发表时间：
2022-04-19
影响因子：
3
通讯作者：
Previtali, Marco
中科院分区：
文献类型：
--
作者：
Ciccolella, Simone;Denti, Luca;Bonizzoni, Paola;Della Vedova, Gianluca;Pirola, Yuri;Previtali, Marco
如COVID-19大流行期间所证明的，能够从每天从多种病毒株产生的越来越多的测序数据中有效地识别变体是至关重要的，以便跟踪病毒株在地球仪中的传播。我们提出了MALVIRUS，一个易于安装和易于使用的应用程序，帮助用户在多个任务所需的分析病毒种群，如SARS-CoV-2。MALVIRUS允许：（1）构建由来自群体序列的一组变异（SNP/插入缺失）组成的变体目录，（2）有效地对由读段样品支持的目录的变体进行基因分型和注释，以及（3）当考虑的病毒物种是SARS-CoV-2时，使用基因分型的变异将输入样品分配给最可能的Pango谱系。对Illumina和Nanopore样本的测试证明了MALVIRUS在分析SARS-CoV-2菌株样本方面的效率和有效性，这些数据来自NCBI提供的公开数据和GISAID提供的更完整的数据集。与最先进工具的比较表明，MALVIRUS总是更精确，并且通常具有更好的回忆。在线版本包含补充材料，可通过10.1186/s12859-022-04668-0获得。
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 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. 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. The online version contains supplementary material available at 10.1186/s12859-022-04668-0.
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影响因子：
5.8
作者：
Denti, Luca;Previtali, Marco;Bonizzoni, Paola
通讯作者：
Bonizzoni, Paola
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DOI：
10.1126/science.abg3055
发表时间：
2021-04-09
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Davies NG;Abbott S;Barnard RC;Jarvis CI;Kucharski AJ;Munday JD;Pearson CAB;Russell TW;Tully DC;Washburne AD;Wenseleers T;Gimma A;Waites W;Wong KLM;van Zandvoort K;Silverman JD;CMMID COVID-19 Working Group;COVID-19 Genomics UK (COG-UK) Consortium;Diaz-Ordaz K;Keogh R;Eggo RM;Funk S;Jit M;Atkins KE;Edmunds WJ
通讯作者：
Edmunds WJ
影响因子：
14.9
作者：
Wilm A;Aw PP;Bertrand D;Yeo GH;Ong SH;Wong CH;Khor CC;Petric R;Hibberd ML;Nagarajan N
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影响因子：
--
作者：
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通讯作者：
Kraemer, Moritz U G
影响因子：
1.9
作者：
Monticelli M;Mele BH;Andreotti G;Cubellis MV;Riccio G
通讯作者：
Riccio G