Accepted for/Published in: JMIR Bioinformatics and Biotechnology
Date Submitted: Jun 24, 2021
Date Accepted: Feb 5, 2022
ESCA pipeline: Easy-to-use SARS-CoV-2 genome Assembler
ABSTRACT
Background:
Early sequencing and quick analysis of SARS-CoV-2 genome are contributing to understand the dynamics of COVID19 epidemics and to design countermeasures at global level.
Objective:
Amplicon-based NGS methods are widely used to sequence the SARS-CoV-2 genome and to identify novel variants that are emerging in rapid succession, 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 ESCA pipeline.
Results:
Our results showed that ESCA could perform high quality genome assembly from IonTorrent and Illumina raw data, and help the user in easily correct low-coverage regions. Moreover, ESCA includes the possibility to compare assembled genomes of multi sample runs through an easy table format.
Conclusions:
In conclusion, ESCA make automatically a variant table output file, fundamental to recognize variants of interest, rapidly. Our pipeline could be a useful method to obtain a rapid, complete and correct analysis also with minimal skill in bioinformatics. The script and manuals are available on GitHub [https://github.com/cesaregruber/ESCA].
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