Text Workflow9/12/2023 Since the Human Genome Project was completed in 2003, Whole-Genome Sequencing (WGS) costs are substantially decreasing over time, which has led to the emergence of new sequencing technologies that empower Next-Generation Sequencing (NGS) based on Sequencing by Synthesis (SBS), Sequencing by Oligo Ligation Detection (SOLiD), Single-Molecule Real-Time (SMRT) sequencing and nanopore-based DNA sequencing. 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. All results are processed and resumed in an interactive HTML report for best data visualization and interpretation. 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. 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. 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. The rapid expansion of Whole-Genome Sequencing has revolutionized the fields of clinical and food microbiology.
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