ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes
ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes
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DOI：
10.1093/bioinformatics/btaa743
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发表时间：
2021-03-01
期刊：
影响因子：
5.8
通讯作者：
Moshiri, Niema
中科院分区：
文献类型：
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作者：
Moshiri, Niema
动机：在分子流行病学中，传播簇的鉴定通常需要病毒基因组序列数据的比对。然而，现有的方法的多序列比对（MSA）的规模差相对于sequence.Results的数量：ViralMSA是一个用户友好的参考引导MSA工具，利用算法技术的读取映射，使MSA的超大型病毒基因组datasets。它与序列数量呈线性关系，能够在几秒钟内对齐数万个完整的病毒基因组。然而，ViralMSA产生的比对省略了相对于参考基因组的插入。
Motivation: In molecular epidemiology, the identification of clusters of transmissions typically requires the alignment of viral genomic sequence data. However, existing methods of multiple sequence alignment (MSA) scale poorly with respect to the number of sequences.Results: ViralMSA is a user-friendly reference-guided MSA tool that leverages the algorithmic techniques of read mappers to enable the MSA of ultra-large viral genome datasets. It scales linearly with the number of sequences, and it is able to align tens of thousands of full viral genomes in seconds. However, alignments produced by ViralMSA omit insertions with respect to the reference genome.