Overview
artic is a pipeline and set of accompanying tools for working with viral nanopore sequencing data, generated from tiling amplicon schemes.
It is designed to help run the artic bioinformatics protocols; for example the SARS-CoV-2 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).
Installation
Via conda
conda install -c bioconda articVia source
1. downloading the source:
Download a release or use the latest master (which tracks the current release):
git clone https://github.com/artic-network/fieldbioinformatics
cd fieldbioinformatics2. installing dependencies:
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 artic3. installing the pipeline:
python setup.py install4. testing the pipeline:
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
Documentation for the artic pipeline is available via read the docs.