%0 Journal Article
%9 ACL : Articles dans des revues avec comité de lecture répertoriées par l'AERES
%A Cherif, Emira
%A Thiam, F. S.
%A Salma, M.
%A Rivera-Ingraham, G.
%A Justy, F.
%A Deremarque, T.
%A Breugnot, D.
%A Doudou, Jean-Claude
%A Gozlan, Rodolphe
%A Combe, Marine
%T ONTdeCIPHER : an amplicon-based nanopore sequencing pipeline for tracking pathogen variants
%D 2022
%L fdi:010084588
%G ENG
%J Bioinformatics
%@ 1367-4803
%M ISI:000774215400035
%N 7
%P 2033-2035
%R 10.1093/bioinformatics/btac043
%U https://www.documentation.ird.fr/hor/fdi:010084588
%> https://www.documentation.ird.fr/intranet/publi/2022-05/010084588.pdf
%V 38
%W Horizon (IRD)
%X 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.
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