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<div align="center"> <h1>ARTIC tools</h1> <h3>a set of tools for working with the ARTIC pipeline</h3> <hr> <a href="https://github.com/will-rowe/artic-tools/actions"><img src="https://github.com/will-rowe/artic-tools/workflows/CI/badge.svg" alt="CI Status" /></a> <a href="https://artic-tools.readthedocs.io/en/latest/?badge=latest"><img src="https://readthedocs.org/projects/artic-tools/badge/?version=latest" alt="Documentation Status"/></a> <a href="https://bioconda.github.io/recipes/artic-tools/README.html"><img src="https://anaconda.org/bioconda/artic-tools/badges/downloads.svg" alt="bioconda"></a> <a href="https://github.com/will-rowe/artic-tools/blob/master/LICENSE"><img src="https://img.shields.io/badge/license-MIT-orange.svg" alt="License"></a> <a href="https://zenodo.org/badge/latestdoi/280260660"><img src="https://zenodo.org/badge/280260660.svg" alt="DOI"></a> </div>

Overview

This collection of tools is being worked on and more utility is due to be added. For now, we have:

download primer schemes and reference sequences
primer scheme validation
alignment softmasking
vcf filtering

Read the docs for more info and checkout the ARTIC pipeline.

Install

conda

conda install -c bioconda artic-tools

source

You need CMake, Boost, HTSlib and a C++17 compiler. To download and install artic-tools run:

git clone --recursive https://github.com/will-rowe/artic-tools.git
mkdir artic-tools/build
cd artic-tools/build
cmake ..
make -j4
make test
../bin/artic-tools -h