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

Installation

Via conda

conda install -c bioconda -c conda-forge artic

Please make sure you are using either mamba or conda version >= 23.10.0 where libmamba solver was made the default conda solver.

Via source

1. downloading the source:

Clone the repository then checkout the 1.4.0-dev branch to test the 1.4.0 pre-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, Please make sure you are using either mamba or conda version >= 23.10.0 where libmamba solver was made the default conda solver. :

conda env create -f environment.yml
conda activate artic

3. installing the pipeline:

pip install .

4. testing the pipeline:

First check the pipeline can be called.

artic -v

You can try the pipeline tests.

./test-runner.sh clair3

For further tests, such as the variant validation tests, check the documentation.

Documentation

Documentation for the artic pipeline is available via read the docs.