Bacterial Genomic Data Analysis in the Next-Generation Sequencing Era.

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• Bacterial genome sequencing is increasingly affordable for research, diagnostics, and clinical microbiology.
• A wide array of genomic data analysis tools exist, but they vary in algorithms, hardware needs, and user interfaces.
• Integrating these tools for sequence data interpretation often demands bioinformatics expertise, which is scarce in many labs.

Purpose of the Study:

• To outline the essential bioinformatics steps for comprehensive bacterial genome analysis using next-generation sequencing data.
• To introduce the Orione framework as a solution for simplifying complex genomic data analysis.
• To enable microbiologists without specialized informatics skills to perform data-intensive analyses.

Main Methods:

• The study covers key bioinformatics processes from raw sequence data to assembled and annotated genomes.
• All described tools are integrated within the Orione framework.
• The framework combines popular open-source bioinformatics tools for microbiology in a transparent manner.

Main Results:

• The Orione framework provides a unified platform for bacterial genome analysis.
• It simplifies the process, making advanced bioinformatics accessible to microbiologists.
• The framework supports analyses from quality control to microbial gene annotation.

Conclusions:

• The Orione framework democratizes bacterial genome analysis by integrating diverse bioinformatics tools.
• It empowers microbiologists to conduct complex computational analyses without extensive informatics training or hardware.
• This approach enhances the accessibility, reproducibility, and transparency of genomic data interpretation in microbiology.