Real-time visualisation dashboard for Oxford Nanopore metagenomic sequencing analysis.
Nanometa Live is the front end for the nanometanf Nextflow pipeline. It monitors taxonomic classification output during sequencing, surfaces detections of pathogens of interest, and provides per-sample quality control and validation views. The application is a single-page Dash web app that runs locally; the analysis itself is delegated to nanometanf.
- Real-time monitoring of cumulative Kraken2 reports during a sequencing run.
- Interactive taxonomic visualisations: Sankey flow and sunburst charts.
- Multi-sample support for barcoded (multiplexed) runs and flat directories.
- Pathogen screening against nine built-in watchlists (clinical pathogens, CDC bioterrorism agents, foodborne, respiratory, drinking water, nosocomial / ESKAPE, wastewater surveillance, zoonotic / One Health, and WHO priority pathogens), with operator-facing alert tiers and recommended actions.
- BLAST identity scoring and minimap2 coverage validation, including
on-demand validation of unexpected detections via Nextflow
-resume. - Quality control panel with nanopore-calibrated thresholds and per-sample filtering statistics.
- Offline deployment workflow: bundle export and import for air-gapped field laboratories, with a pre-flight readiness checker.
- Web-based control of pipeline lifecycle (start, stop, configure) for operators without command-line access.
- Quick start with nanorunner -- end-to-end demo using simulated input.
- Local / server test guide -- pre-release validation of batch and real-time modes with nanorunner.
- User guide -- full reference, including installation, configuration, and tab-by-tab walkthrough.
- Operator guide -- field-deployment reference and decision trees.
Tabs are grouped by workflow: an Analysis group for monitoring a run and a Setup group for configuring and preparing one.
| Tab | Group | Purpose |
|---|---|---|
| Dashboard | Overview | Run status, pathogen alerts, sample summary, classification overview |
| Organisms | Analysis | Detected organisms with abundance, confidence, and watchlist flags |
| Quality Control | Analysis | Nanopore-calibrated metrics and filtering statistics |
| Taxonomy | Analysis | Sankey flow and sunburst views for taxonomic exploration |
| Validation | Analysis | BLAST identity scores and minimap2 coverage plots |
| Configuration | Setup | Analysis settings, pipeline control, save and load configurations |
| Watchlist & Preparation | Setup | Built-in watchlists and custom imports, reference-genome download and BLAST-database build, readiness checks |
| Deployment | Setup | Offline bundle export and import for air-gapped field laboratories |
Python 3.11+ and, for the dashboard, the core runtime stack:
dash>=4.0.0
dash-ag-grid>=31.0.0
dash-bootstrap-components>=1.7.1
plotly>=6.0.0
pandas>=2.2.3
numpy>=2.0.0
biopython>=1.85
diskcache>=5.6.0
psutil>=6.0.0
The complete, authoritative list (including the background-callback and
export dependencies) is in requirements.txt and is
installed automatically by pip install.
For pipeline execution: Nextflow 26.04.0 or later (the version nanometanf
floors at). Container engines are not required; nanometanf runs under the
conda profile by default.
Nanometa Live and nanometanf are released together. A GUI release sends
parameters that only its companion pipeline declares, and Start Analysis
refuses an older checkout by version. remote:dev runs the checkout under
the launch's Nextflow home (<results directory>/.nextflow for a GUI Start
unless NXF_HOME is set); the refusal message names the nextflow pull
command for that home.
| Nanometa Live | nanometanf | Nextflow |
|---|---|---|
| 0.19.x | 1.11.0 | >= 26.04.0 |
| 0.18.x | 1.10.0 | >= 26.04.0 |
| 0.17.x | 1.9.0 | >= 26.04.0 |
| 0.16.x | 1.8.0 | >= 26.04.0 |
Earlier pairings are recorded in CHANGELOG.md.
The test suite needs the runtime dependencies (Dash, Plotly, pandas), so install the package with its dev extras into a virtual environment:
pip install -e ".[dev]"
pytest # full suite, parallel (pytest-xdist)
pytest -n 0 # serial, for pdb/print debugging
pytest --cov=nanometa_live --cov-report=term-missing # with coverage gate
Tests marked slow need Nextflow/conda and are skipped by default; run them
with pytest -m slow. CI runs the suite and the coverage gate on Python 3.11
and 3.12 for every push and pull request to main and dev.
If you use Nanometa Live in research, please cite:
Sandas K, Lewerentz J, Karlsson E, et al. Nanometa Live: a user-friendly application for real-time metagenomic data analysis and pathogen identification. Bioinformatics. 2024;40(3):btae108. doi:10.1093/bioinformatics/btae108
GNU General Public License v3.0. See LICENSE.