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Only_obitools pipeline
======================

# Table of contents

1. [Introduction](#1-introduction)
2. [Installation](#2-installation)
  1. [Requirements](#21-requirements)
  2. [Optional components](#22-optional-components)
3. [Reporting bugs](#3-reporting-bugs)
4. [Running the pipeline](#4-running-the-pipeline)

-----------------

# 1. Introduction

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Here, we reproduce the bioinformatics pipeline used by [SPYGEN](http://www.spygen.com/) to generate species environmental presence from raw eDNA data. This pipeline is based on [OBItools](https://git.metabarcoding.org/obitools/obitools/wikis/home) a set of python programs designed to analyse Next Generation Sequencer outputs (illumina) in the context of DNA Metabarcoding.
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# 2. Installation

You will need to install 

## 2.1. Requirements

In order to run "only_obitools", you need a couple of programs. Most of
them should be available pre-compiled for your distribution. The
programs and libraries you absolutely need are:

- [OBItools](https://pythonhosted.org/OBITools/welcome.html#installing-the-obitools)


## 2.2. Optional components

Other libraries are optional and only limit the features that are
built. These include:


# 3. Reporting bugs

If you're sure you've found a bug — e.g. if one of my programs crashes
with an obscur error message, or if the resulting file is missing part
of the original data, then by all means submit a bug report.

I use [GitLab's issue system](https://gitlab.com/edna/only_obitools/issues)
as my bug database. You can submit your bug reports there. Please be as
verbose as possible — e.g. include the command line, etc

# 4. Running the pipeline

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Quickstart

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1. create a new folder for nextflow to work in
2. switch to this new folder    
3. open a shell
4. type in `curl -fsSL get.nextflow.io | bash` to download nextflow into this folder
5. make sure that the programs stated in the Requirements section below are installed on your machine. After nextflow is downloaded, replace all the "YOUR_***" parts in the following command with your own paths
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6. run your command : `./nextflow run main.nf`
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that's it ! The pipeline is running and crunching your data. Look for the overview.txt or. overview_new.txt in your output folder after the pipeline is finished
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