Open AccessThe Easy-to-Use SARS-CoV-2 Assembler for Genome Sequencing: Development Study
Author(s) -
Martina Rueca,
Emanuela Giombini,
Francesco Messina,
Barbara Bartolini,
Antonino Di,
Maria Rosaria Capobianchi,
Cesare Ernesto Maria Gruber
Publication year - 2022
Publication title -
jmir bioinformatics and biotechnology
Language(s) - English
Resource type - Journals
ISSN - 2563-3570
DOI - 10.2196/31536
Subject(s) - genome , sequence assembly , amplicon , amplicon sequencing , pipeline (software) , computational biology , dna sequencing , ion semiconductor sequencing , computer science , covid-19 , whole genome sequencing , table (database) , biology , genetics , data mining , gene , polymerase chain reaction , infectious disease (medical specialty) , operating system , medicine , gene expression , transcriptome , 16s ribosomal rna , disease , pathology
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.