@article{fdi:010084588,
  title = {{ONT}de{CIPHER} : an amplicon-based nanopore sequencing pipeline for tracking pathogen variants},
  author = {{C}herif, {E}mira and {T}hiam, {F}. {S}. and {S}alma, {M}. and {R}ivera-{I}ngraham, {G}. and {J}usty, {F}. and {D}eremarque, {T}. and {B}reugnot, {D}. and {D}oudou, {J}ean-{C}laude and {G}ozlan, {R}odolphe and {C}ombe, {M}arine},
  editor = {},
  language = {{ENG}},
  abstract = {{M}otivation: {A}mplicon-based nanopore sequencing is increasingly used for molecular surveillance during epidemics (e.g. {ZIKA}, {EBOLA}) or pandemics (e.g. {SARS}-{C}o{V}-2). {H}owever, 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 {SNP}s effect to phylogenetic analysis. {R}esults: {H}ere, we present {ONT}de{CIPHER}, an amplicon-based {O}xford {N}anopore {T}echnology sequencing pipeline to analyze the genetic diversity of {SARS}-{C}o{V}-2 and other pathogens. {O}ur pipeline integrates 13 bioinformatics tools. {W}ith 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. {A}vailability and implementation: {ONT}de{CIPHER} is available at https://github.com/emiracherif/{ONT}de{CIPHER}. {C}ontact: emira.cherif@ird.fr {S}upplementary information: {S}upplementary data are available at {B}ioinformatics online.},
  keywords = {},
  booktitle = {},
  journal = {{B}ioinformatics},
  volume = {38},
  numero = {7},
  pages = {2033--2035},
  ISSN = {1367-4803},
  year = {2022},
  DOI = {10.1093/bioinformatics/btac043},
  URL = {https://www.documentation.ird.fr/hor/fdi:010084588},
}