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1. Introduction
Nanometa Live is a specialized tool engineered for real-time metagenomic analysis, specifically designed to work with Oxford Nanopore sequencing technologies. The system is comprised of a backend pipeline for data processing and a frontend graphical user interface (GUI) for intuitive data visualization.
The backend utilizes a Snakemake workflow that initiates processing as soon as the Oxford Nanopore basecaller starts generating batch files. The following steps are executed:
- Quality Filtering: The initial fastq.gz files undergo cleaning and filtering using FastP.
- Kraken2 Classification: Filtered reads are then classified using Kraken2.
- Quality Control: Metrics such as timestamps, read counts, and the number of base pairs are extracted for quality control.
- BLAST Validation: Reads from user-defined species (often pathogens) are cross-validated using BLAST against reference genomes.
New Feature: The backend now utilizes a single YAML file for environment setup, eliminating the need for continuous internet access.
The GUI is a web-based Dash application tailored for an optimal user experience. It updates at user-defined intervals and provides real-time insights into:
- Overall Species Composition: An overview of the microbial community present in the sample.
- Pathogen Monitoring: User-defined species of interest are prominently highlighted.
New Feature: The GUI now includes options for direct saving of plots and secure workflow termination, further enhancing its user-friendliness.
The program has been developed and tested on Ubuntu 22.04.2 LTS and macOS but should be compatible with any Linux distribution.