README.md

ARTIC

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

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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 -c conda-forge artic

If conda reports that nothing provides particular packages when running the above command ensure your channel_priority is set to flexible using the following command:

conda config --set channel_priority false

Via 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 fieldbioinformatics

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. installing the pipeline:

python setup.py install

4. 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.