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Introduction
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: Basics of ONTOLOGY
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: Choosing a workflow
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: Choosing a mode
For installation requirements, please see: Installation