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Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
Published on: March 11, 2020
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ONTdeCIPHER: an amplicon-based nanopore sequencing pipeline for tracking pathogen variants.
Emira Cherif1, Fatou Seck Thiam1, Mohammad Salma2,3
1ISEM, Univ Montpellier, CNRS, IRD, 34090 Montpellier, France.
Bioinformatics (Oxford, England)
|January 26, 2022
Summary
ONTdeCIPHER is a new pipeline for analyzing pathogen genetic diversity using Oxford Nanopore Technology sequencing. This tool simplifies complex bioinformatics tasks for molecular surveillance, aiding in epidemic and pandemic response.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Amplicon-based nanopore sequencing is crucial for pathogen surveillance during epidemics and pandemics.
- Existing tools often require advanced bioinformatics expertise, limiting accessibility for researchers.
Purpose of the Study:
- To present ONTdeCIPHER, a user-friendly pipeline for amplicon-based Oxford Nanopore Technology sequencing data analysis.
- To enable comprehensive downstream analysis for pathogen genetic diversity studies.
Main Methods:
- Integration of 13 distinct bioinformatics tools into a single pipeline.
- Development of a simple command-line interface and configuration file for ease of use.
Main Results:
- ONTdeCIPHER automates data pre-processing, quality assessment, and variant calling.
- The pipeline facilitates consensus genome reconstruction, variant effect prediction, lineage inference, and phylogenetic analysis.
- Successful application for analyzing SARS-CoV-2 genetic diversity.
Conclusions:
- ONTdeCIPHER provides a versatile and accessible solution for pathogen genomic surveillance.
- The pipeline empowers researchers with limited bioinformatics experience to conduct in-depth genetic analysis.
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