The artic pipeline
is designed to help run the artic bioinformatics protocols; for example the nCoV-2019 novel coronavirus protocol.
Features include:
- read filtering
- primer trimming
- amplicon coverage normalisation
- variant calling
- consensus building
There are 2 workflows baked into this pipeline, one which uses signal data (via nanopolish) and one that does not (via medaka).
conda install -c bioconda artic
git clone https://github.com/artic-network/fieldbioinformatics
cd fieldbioinformatics
python setup.py install
The artic pipeline
has several software dependencies. You can solve these dependencies using the minimal conda environment we have provided:
conda env create -f environment.yml
conda activate artic
First check the pipeline can be called.
artic -v
You can try the pipeline tests.
./test-runner.sh nanopolish
./test-runner.sh medaka
For further tests, such as the variant validation tests, check the documentation.
Documentation for the artic pipeline
is available via read the docs.
For nCov work, see the SOP on the artic website.