ARTIC pipeline

a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore

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Overview

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).

Installation

Via conda

conda install -c bioconda artic

Via source

1. installing the pipeline:

git clone https://github.com/artic-network/fieldbioinformatics
cd fieldbioinformatics
python setup.py install

2. 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 artic

3. 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.

For nCov work, see the SOP on the artic website.