Skip to content

GitLab

  • Menu
Projects Groups Snippets
    • Loading...
  • Help
    • Help
    • Support
    • Community forum
    • Submit feedback
    • Contribute to GitLab
  • Sign in
  • snakemake_rapidrun_obitools snakemake_rapidrun_obitools
  • Project information
    • Project information
    • Activity
    • Labels
    • Planning hierarchy
    • Members
  • Repository
    • Repository
    • Files
    • Commits
    • Branches
    • Tags
    • Contributors
    • Graph
    • Compare
  • Issues 7
    • Issues 7
    • List
    • Boards
    • Service Desk
    • Milestones
  • Merge requests 0
    • Merge requests 0
  • CI/CD
    • CI/CD
    • Pipelines
    • Jobs
    • Schedules
  • Deployments
    • Deployments
    • Environments
    • Releases
  • Monitor
    • Monitor
    • Incidents
  • Packages & Registries
    • Packages & Registries
    • Container Registry
  • Analytics
    • Analytics
    • Value stream
    • CI/CD
    • Repository
  • Wiki
    • Wiki
  • Snippets
    • Snippets
  • Activity
  • Graph
  • Create a new issue
  • Jobs
  • Commits
  • Issue Boards
Collapse sidebar
  • edna
  • snakemake_rapidrun_obitoolssnakemake_rapidrun_obitools
  • Wiki
  • Home

Last edited by mbruno Mar 14, 2022
Page history

Home

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.

⚠ The wiki is being revised. ⚠

Table of contents

  1. Introduction
  2. Tutorial *In development*

. Note pour les redacteurs

Edit sidebar

Clone repository
  1. Introduction

  2. Tutorial *In development*

. Archive

  1. Let's get started

    2.1. Installation

    2.2. Tutorial

    2.2.1. RAPIDRUN analysis

    2.2.2. CLASSIC analysis

  2. How-to guides

  3. Reference

    4.1. Workflow management

    4.2. Wildcards

    4.3. Workflow architecture

    4.4. Rules description

    4.5. Environments

  4. Explanation

. Note pour les redacteurs

Edit sidebar