Nomadic is a real-time bioinformatics pipeline and dashboard for nanopore sequencing data. While sequencing is still ongoing, it performs read mapping and sample quality control, as well as variant calling and annotation. This information is displayed in real-time to a graphical dashboard that has interactive features.
Please visit our documentation to learn more.
- Real-time read mapping with Minimap2.
- Real-time sample quality control and amplicon coverage evaluation.
- Real-time variant calling with bcftools or delve (our own variant caller). These calls are preleiminary; treat with caution.
- Support for different reference genomes or amplicons panels.
Nomadic can be installed from bioconda
conda install bioconda::nomadic
Navigate to a directory where your nomadic files should live and setup a workspace with
nomadic start pfalciparum
Afterwards, navigate to the newly created workspace, create a metadata file and start your experiment:
cd nomadic
nomadic realtime <expt_name>
For more detailed information, see our documentation.
If you would like to develop Nomadic you can install it from source. First, clone the github repository
git clone https://github.com/JasonAHendry/nomadic.git
and then create the development conda environment, and activated it:
conda env create -f environments/dev.yml
conda activate nomadic-dev
Finally, install the package locally in development mode:
pip install -e .
Please note that if new dependencies are added, you will have to update your conda environment. For this, run:
conda env update -f environments/dev.yml
To test Nomadic, we have written a small python script that simulates nanopore sequencing:
python scripts/simulate_sequencing.py
This will move FASTQ files into the directory example_data/minknow/fastq_pass, which you can process with nomadic realtime.
Additionally, if you followed our development instructions you can test with:
pytest
The documentation was created using MkDocs. You can serve it locally with:
conda env create -f environments/dev.yml
mkdocs serve
This work was funded by the Bill and Melinda Gates Foundation (INV-003660, INV-048316).