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. 2022 Mar 14;3(1):e31536.
doi: 10.2196/31536. eCollection 2022 Jan-Dec.

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

Martina Rueca  1 , Emanuela Giombini  1 , Francesco Messina  2 , Barbara Bartolini  2 , Antonino Di Caro  2   3 , Maria Rosaria Capobianchi  1   3 , Cesare Em Gruber  1
Affiliations

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

Martina Rueca et al. JMIR Bioinform Biotechnol. .

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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Conflict of interest statement

Conflicts of Interest: None declared.

Figures

Figure 1
Figure 1
Classification scheme for genome assemblers, in which assembled genome sequences (SEQ) were compared with the corresponding submitted sequences (on GISAID) and with reference genome sequence “Wuhan-Hu-1” (REF). Nucleotide threesomes were classified using the following 11 categories: false deletion (Fd), false insertion (Fi), false negative (FN), false positive (FP), mutation error (Me), N correct (Nc), N error (Ne), true deletion (Td), true insertion (Ti), true negative (TN), true positive (TP).
Figure 2
Figure 2
Comparison of true positive mutations between our Easy-to-use SARS-CoV-2 Assembler (ESCA) and the (A) Illumina DRAGEN tool and (B) iterative refinement meta-assembler (IRMA) recommended by Ion Torrent.
See this image and copyright information in PMC

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