Rueca Martina, Giombini Emanuela, Messina Francesco, Bartolini Barbara, Di Caro Antonino, Capobianchi Maria Rosaria, Gruber Cesare Em
Laboratory of Virology and Biosafety Laboratories National Institute for Infectious Diseases "Lazzaro Spallanzani" Istituto di Ricovero e Cura a Carattere Scientifico Rome Italy.
Laboratory of Microbiology and Biological Bank National Institute for Infectious Diseases "Lazzaro Spallanzani" Istituto di Ricovero e Cura a Carattere Scientifico Rome Italy.
JMIR Bioinform Biotechnol. 2022 Mar 14;3(1):e31536. doi: 10.2196/31536. eCollection 2022 Jan-Dec.
Early sequencing and quick analysis of the SARS-CoV-2 genome have contributed to the understanding of the dynamics of COVID-19 epidemics and in designing countermeasures at a global level.
Amplicon-based next-generation sequencing (NGS) methods are widely used to sequence the SARS-CoV-2 genome and to identify novel variants that are emerging in rapid succession as well as harboring multiple deletions and amino acid-changing mutations.
To facilitate the analysis of NGS sequencing data obtained from amplicon-based sequencing methods, here, we propose an easy-to-use SARS-CoV-2 genome assembler: the Easy-to-use SARS-CoV-2 Assembler (ESCA) pipeline.
Our results have shown that ESCA could perform high-quality genome assembly from Ion Torrent and Illumina raw data and help the user in easily correct low-coverage regions. Moreover, ESCA includes the possibility of comparing assembled genomes of multisample runs through an easy table format.
In conclusion, ESCA automatically furnished a variant table output file, fundamental to rapidly recognizing variants of interest. Our pipeline could be a useful method for obtaining a complete, rapid, and accurate analysis even with minimal knowledge in bioinformatics.
对严重急性呼吸综合征冠状病毒2（SARS-CoV-2）基因组的早期测序和快速分析有助于了解2019冠状病毒病（COVID-19）疫情的动态，并有助于在全球范围内设计应对措施。
基于扩增子的下一代测序（NGS）方法被广泛用于对SARS-CoV-2基因组进行测序，并识别快速出现的新变体以及带有多个缺失和氨基酸变化突变的变体。
为便于分析从基于扩增子的测序方法获得的NGS测序数据，在此，我们提出一种易于使用的SARS-CoV-2基因组组装工具：易于使用的SARS-CoV-2组装工具（ESCA）流程。
我们的结果表明，ESCA可以从Ion Torrent和Illumina原始数据进行高质量的基因组组装，并帮助用户轻松校正低覆盖区域。此外，ESCA还包括通过简单的表格格式比较多样本运行的组装基因组的可能性。
总之，ESCA自动提供一个变体表格输出文件，这对于快速识别感兴趣的变体至关重要。即使对生物信息学了解甚少，我们的流程也可能是获得完整、快速和准确分析的有用方法。
