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Home
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Introduction
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Welcome to the manual for ONTOLOGY, an end-to-end platform for **DNA Barcoding** and **Metabarcoding** workflows, including sample preparation, processing, and bioinformatic analysis. 
The full ONTOLOGY workflow (kit mode) is designed to seamlessly link the laboratory and computational preparation phases by providing freeze-dried PCR microplates, designed specifically for easy sample tracking and direct software input. Users without ONTOLOGY kits may prepare their own plates and still use ONTOLOGY's custom **DNA Barcoding** and **Metabarcoding** bioinformatic analysis pipelines (Custom Mode). For more information on the basics of ONTOLOGY does, please see: :ref:`Basics of ONTOLOGY <about>`

The **DNA Barcoding** workflow is designed to facilitate sequencing of *individual specimens*. The **Metabarcoding** workflow is designed to facilitate sequencing of *samples containing DNA from many specimens*, including eDNA analysis. The same ONTOLOGY plates can be used for either workflow. For more information on the two workflows, please see: :ref:`Choosing a workflow <FEATURES_OF_BARCODING_AND_METABARCODING>`

The **DNA Barcoding** and **Metabarcoding** workflows share similar steps. **PREPARE** establishes the run and sample metadata; **IMPLEMENT** (DNA Barcoding only) guides the user through molecular laboratory protocols; **ANALYZE** performs bioinformatic analysis and data upload to `BOLD`_ (**DNA Barcoding**) or RAMS (**Metabarcoding**; under development). Both workflows have beginner workflows designed to teach researchers new to barcoding all aspects of the protocols. They each also have **advanced user** modes, accessible via the ONTOLOGY 'DNA double helix' logo. We note where the protocols diverge. For more information on the different modes of ONTOLOGY, please see: :ref:`Choosing a mode <ABOUT_DIFFERENT_MODES>`

For installation requirements, please see: :ref:`Installation <installation>`


.. _BOLD: https://boldsystems.org/



Page tree
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.. toctree::
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    getting-started
    tutorials
    workflow
    uploading-to-BOLD
    reference
    help