ONTdeCIPHER: an amplicon-based nanopore sequencing pipeline for tracking pathogen variants.
Bioinformatics
; 38(7): 2033-2035, 2022 03 28.
Article
in En
| MEDLINE
| ID: mdl-35080622
ABSTRACT
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. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Zika Virus
/
Zika Virus Infection
/
Nanopore Sequencing
/
COVID-19
Limits:
Humans
Language:
En
Journal:
Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2022
Type:
Article
Affiliation country:
France