Cherif Emira, Thiam F. S., Salma M., Rivera-Ingraham G., Justy F., Deremarque T., Breugnot D., Doudou Jean-Claude, Gozlan Rodolphe, Combe Marine. (2022). ONTdeCIPHER : an amplicon-based nanopore sequencing pipeline for tracking pathogen variants. Bioinformatics, 38 (7), p. 2033-2035. ISSN 1367-4803.
Titre du document
ONTdeCIPHER : an amplicon-based nanopore sequencing pipeline for tracking pathogen variants
Année de publication
2022
Auteurs
Cherif Emira, Thiam F. S., Salma M., Rivera-Ingraham G., Justy F., Deremarque T., Breugnot D., Doudou Jean-Claude, Gozlan Rodolphe, Combe Marine
Source
Bioinformatics, 2022,
38 (7), p. 2033-2035 ISSN 1367-4803
Motivation: Amplicon-based nanopore sequencing is increasingly used for molecular surveillance during epidemics (e.g. ZIKA, EBOLA) or pandemics (e.g. SARS-CoV-2). However, there is still a lack of versatile and easy-to-use tools that allow users with minimal bioinformatics skills to perform the main steps of downstream analysis, from quality testing to SNPs effect to phylogenetic analysis. Results: Here, we present ONTdeCIPHER, an amplicon-based Oxford Nanopore Technology sequencing pipeline to analyze the genetic diversity of SARS-CoV-2 and other pathogens. Our pipeline integrates 13 bioinformatics tools. With a single command line and a simple configuration file, users can pre-process their data and obtain the sequencing statistics, reconstruct the consensus genome, identify variants and their effects for each viral isolate, infer lineage and, finally perform multi-sequence alignments and phylogenetic analyses. Availability and implementation: ONTdeCIPHER is available at https://github.com/emiracherif/ONTdeCIPHER. Contact: emira.cherif@ird.fr Supplementary information: Supplementary data are available at Bioinformatics online.
Plan de classement
Sciences fondamentales / Techniques d'analyse et de recherche [020]
;
Entomologie médicale / Parasitologie / Virologie [052]
;
Informatique [122]
Localisation
Fonds IRD [F B010084588]
Identifiant IRD
fdi:010084588
