RT info:eu-repo/semantics/article
T1 CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter
A1 Ortega Sanz, Irene
A1 Barbero Aparicio, José Antonio
A1 Canepa Oneto, Antonio Jesús
A1 Rovira Carballido, Jordi
A1 Melero Gil, Beatriz
K1 Pipeline
K1 Comparative genomics
K1 Genome analysis
K1 Bacterial typing
K1 Genome annotation
K1 Virulence genes
K1 Antimicrobial resistance genes
K1 Microbiología
K1 Microbiology
K1 Genómica
K1 Genomics
K1 Salud pública
K1 Public health
AB Background: The rapid expansion of Whole-Genome Sequencing has revolutionized the fields of clinical and food microbiology. However, its implementation as a routine laboratory technique remains challenging due to the growth of data at a faster rate than can be effectively analyzed and critical gaps in bioinformatics knowledge.Results: To address both issues, CamPype was developed as a new bioinformatics workflow for the genomics analysis of sequencing data of bacteria, especially Campylobacter, which is the main cause of gastroenteritis worldwide making a negative impact on the economy of the public health systems. CamPype allows fully customization of stages to run and tools to use, including read quality control filtering, read contamination, reads extension and assembly, bacterial typing, genome annotation, searching for antibiotic resistance genes, virulence genes and plasmids, pangenome construction and identification of nucleotide variants. All results are processed and resumed in an interactive HTML report for best data visualization and interpretation.Conclusions: The minimal user intervention of CamPype makes of this workflow an attractive resource for microbiology laboratories with no expertise in bioinformatics as a first line method for bacterial typing and epidemiological analyses, that would help to reduce the costs of disease outbreaks, or for comparative genomic analyses. CamPype is publicly available at https://github.com/JoseBarbero/CamPype.
PB Springer
YR 2023
FD 2023-07
LK https://hdl.handle.net/10259/11243
UL https://hdl.handle.net/10259/11243
LA eng
NO The project leading to these results received funding from “La Caixa” Foundation and Caja Burgos Foundation, under agreement LCF/PR/PR18/51130007. Irene Ortega-Sanz received a predoctoral grant from the Junta of Castile and León, cofinanced by the Ministry of Education of the Government of Castile and León and the European Social Fund. José A. Barbero-Aparicio was founded through a pre-doctoral grant from the University of Burgos.
DS Repositorio Institucional de la Universidad de Burgos
RD 21-abr-2026