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Nanometa Live: a user-friendly application for real-time metagenomic data analysis and pathogen identification
Kristofer Sandås1, Jacob Lewerentz1, Edvin Karlsson1
1Division of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå 906 21, Sweden.
Bioinformatics (Oxford, England)
|February 26, 2024
Summary
Nanometa Live offers real-time metagenomic analysis and pathogen identification using portable sequencing devices. This tool provides an efficient, user-friendly interface for on-site data interpretation without continuous internet access.
Area of Science:
- Bioinformatics
- Genomics
- Microbiology
Background:
- Metagenomic analysis is crucial for understanding microbial communities and identifying pathogens.
- Real-time analysis of metagenomic data can accelerate research and clinical diagnostics.
- Existing tools often require constant internet or server connectivity, limiting on-site applications.
Purpose of the Study:
- To develop a user-friendly, real-time metagenomic data analysis and pathogen identification tool.
- To enable efficient interpretation of metagenomic data generated by Oxford Nanopore Technologies (ONT) sequencing platforms.
- To provide a portable solution for on-site metagenomic analysis.
Main Methods:
- Developed Nanometa Live as a local web application using the Dash framework.
- Integrated Snakemake for efficient data processing.
- Implemented automated BLAST validation and custom Kraken2 database handling.
- Ensured portability and ease of use through containerization (Docker, Singularity).
Main Results:
- Nanometa Live provides a simplified graphical user interface for real-time metagenomic data visualization and interpretation.
- The tool supports analysis from ONT MinION and Flongle flow cells.
- It allows for the detection of user-defined pathogens and provides a comprehensive taxonomic composition view.
- The application can operate offline after initial installation.
Conclusions:
- Nanometa Live offers an efficient and accessible solution for real-time metagenomic analysis and pathogen identification.
- Its offline capability and user-friendly design make it suitable for both research and clinical settings.
- The tool enhances the utility of portable sequencing technologies for on-site genomic applications.
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