README.md

## eDNA-seq Metabarcoding OTU-clustering pipeline

**eDNA-seq Metabarcoding OTU-clustering** is a bioinformatics pipeline built using Snakemake, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

## Introduction

**eDNA-seq Metabarcoding OTU-clustering** is specifically used for the analysis of environmental DNA metabarcoding NGS data, demultiplexing, filtering and clustering sequences in Operational Taxonomic Unit (OTU).

This pipeline has been initially tested with marine environment samples, using molecular markers such as Teleo1. The workflow should work with any organisms and environment. It is proven for large-scale data analysis.

OTU-clustering steps are based on [TARA Fred's metabarcoding pipeline](https://github.com/frederic-mahe/swarm/wiki/Fred%27s-metabarcoding-pipeline).


## Method

The wofklows processes raw data from fastq inputs (FastQC), merges paired-end reads together (vsearch), applies complex demultiplexing based on notice provided by the sequencing platform, primer clipping (cutadapt), sample dereplication (vsearch), sequencing quality extraction, clusters sequences in OTU (swarm), detects chimera (vsearch) and assign taxonomy to each OTU (NCBI taxonomy; ecotag; obitools). Ultimately, OTU tables with and without taxonomy assignments are generated. See the output documentation for more details.


## Workflow



1. [Installation]()
2. Pipeline configuration
    * [Local installation]()
    * [Adding your own system config]()
    * [Parameters]()
3. [Running the pipeline]()
    * [Quick start]()
    * [Basic run]()
    * [Reproducibility]()
    * [Input files]()
    * [Config file]()
    * [step 1...]()
    * [step2...]()
4. [Output results]()
5. [How-to guide]()
6. [Reference]()
7. [Metabarcoding context - discussion to go further]()

## Credits

**eDNA-seq Metabarcoding OTU-clustering** was coded and written by Virginie Marques and Pierre-Edouard Guerin.

We thank the following people for their help in the development of this pipeline:

* Agnes Duhamet
* Alice Valentini
* Apolline Gorry
* Bastien Mace
* David Mouillot
* Emilie Boulanger
* Laetitia Mathon
* Laura Benestan
* Stephanie Manel
* Tony Dejean


## Contributions and Support

:bug: If you are sure you have found a bug, then by all means submit a bug report. You can submit your bug reports on Gitlab [here](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/issues).



For further information or help, don't hesitate to get in touch on Slack (you can join with this invite).

[![Get help on Slack](https://img.shields.io/badge/slack-cefebev%23metabarcoding_otu-4A154B?logo=slack)](https://cefebev.slack.com/archives/C01NYK8B9K7)


## Citations

You can cite the **eDNA-seq Metabarcoding OTU-clustering** publication as follows:

```
Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences

Virginie Marques, Pierre‐Édouard Guerin, Mathieu Rocle, Alice Valentini, Stephanie Manel, David Mouillot, Tony Dejean

Molecular Ecography. 2020 Aug 04. doi:  https://doi.org/10.1111/ecog.05049.
```