Run automatic and parallelized analysis of metabarcoding sequencing data

This is a powerful, extensible, and decentralized metabarcoding sequencing data analysis package with a focus on data and analysis transparency. This enables researchers to start an analysis with raw DNA sequence data and finish with table of species occurrence by sample.

Here we take advantage of snakemake to set a framework which automates metabarcoding analysis using obitools. This framework manages dependencies so you don't need to install obitools because the framework will do this work for you. It eases to set parameters by filling a configuration file, so that you can run many times the same analysis with different parameters.

Finally the framework can handle various dataset of sequencing data such as RAPIDRUN.

⚠ The current workflow is more easy to use and the wiki is obsolete at the moment. The up to date version of the wiki will be delivered in May 2021 the latest. ⚠

Table of contents

1. Introduction

2. Let's get started

   2.1. Installation

   2.2. Tutorial

   2.2.1. RAPIDRUN analysis

   2.2.2. CLASSIC analysis

3. How-to guides

4. Reference

   4.1. Workflow management

   4.2. Wildcards

   4.3. Workflow architecture

   4.4. Rules description

   4.5. Environments

5. Explanation

. Note pour les redacteurs

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