2026-11-03T00:57:54Zhttps://riubu.ubu.es/oai/request

oai:riubu.ubu.es:10259/112432026-01-21T01:05:29Zcom_10259_4292com_10259_5086com_10259_2604col_10259_4293

00925njm 22002777a 4500 dc Ortega Sanz, Irene author Barbero Aparicio, José Antonio author Canepa Oneto, Antonio Jesús author Rovira Carballido, Jordi author Melero Gil, Beatriz author 2023-07 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. https://hdl.handle.net/10259/11243 10.1186/s12859-023-05414-w 1471-2105 Pipeline Comparative genomics Genome analysis Bacterial typing Genome annotation Virulence genes Antimicrobial resistance genes CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter