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The Easy-to-Use SARS-CoV-2 Assembler for Genome Sequencing: Development Study

Martina Rueca¹, Emanuela Giombini¹, Francesco Messina²

¹Laboratory of Virology and Biosafety Laboratories National Institute for Infectious Diseases "Lazzaro Spallanzani" Istituto di Ricovero e Cura a Carattere Scientifico Rome Italy.

JMIR Bioinformatics and Biotechnology

|March 21, 2022

Abstract

Background:

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.

Objective:

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.

Methods:

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.

Results:

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.

Conclusions:

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.

Keywords:

COVID-19 NGS data analysis SARS-CoV-2 genome algorithms bioinformatic bioinformatics tool digital tools genome health informatics

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