coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies
coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies
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DOI：
10.1093/bioinformatics/btab597
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发表时间：
2021-08-18
期刊：
影响因子：
5.8
通讯作者：
Korobeynikov, Anton
中科院分区：
文献类型：
--
作者：
Meleshko, Dmitry;Hajirasouliha, Iman;Korobeynikov, Anton
动机：COVID-19大流行引发了对病毒研究，特别是冠状病毒研究的广泛科学兴趣。天然病毒库中病毒种类的鉴定和表征通常涉及从头组装。然而，现有的基因组、宏基因组和转录组组装器往往无法将许多病毒（包括冠状病毒）组装成一个单一的基因组。数据集之间和数据集内部的覆盖变化，紧密菌株的存在，剪接变体和污染为组装者处理具有不同属性的病毒数据集设置了很高的门槛。结果：我们开发了coronaSPAdes，这是一种用于RNA病毒物种恢复的新型组装体，特别是冠状病毒。coronaSPAdes利用有关病毒基因组结构的知识来改进最初在生物合成spades中实施的组装扩展想法。我们已经证明，coronaSPAdes在恢复全长RNA病毒基因组方面优于现有的SPAdes模式和其他流行的短读宏基因组和病毒组装器。
Motivation: The COVID-19 pandemic has ignited a broad scientific interest in viral research in general and coronavirus research in particular. The identification and characterization of viral species in natural reservoirs typically involves de novo assembly. However, existing genome, metagenome and transcriptome assemblers often are not able to assemble many viruses (including coronaviruses) into a single contig. Coverage variation between datasets and within dataset, presence of close strains, splice variants and contamination set a high bar for assemblers to process viral datasets with diverse properties.Results: We developed coronaSPAdes, a novel assembler for RNA viral species recovery in general and coronaviruses in particular. coronaSPAdes leverages the knowledge about viral genome structures to improve assembly extending ideas initially implemented in biosyntheticSPAdes. We have shown that coronaSPAdes outperforms existing SPAdes modes and other popular short-read metagenome and viral assemblers in the recovery of full-length RNA viral genomes.