CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter.

ABSTRACT:

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, b

SUBMITTER: Ortega-Sanz I 

PROVIDER: S-EPMC10357626 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature