Objective & Concept
Objective
This workflow provides guidance on the data management aspects of eDNA research. It can help both individual analyses and entire research projects to manage data effectively. It can also be used to quickly and easily introduce new staff members to the process (often called ‘onboarding’).
This workflow is complementary to a Data Management Plan (DMP) and is intended to be appended as an annex to the DMPs of projects that follow this workflow. INBO is working on eDNA-research focused DMP-templates, which will also be compatible with this workflow. We hope to make these freely available in the future, but don’t let that hold you back from making your own! They can save a lot of time when research projects with significant overlaps are carried out.
The steps in the workflow are important for all people involved in eDNA research. Who carries out which checkpoint must be agreed upon among team members, ideally before the research begins.
Concept
When thinking about a project proposal or research idea, and especially when beginning to write up it’s design, scope etc. is also the perfect time to start your DMP. Many of the steps that need to be taken to organise data management also form part of a DMP, and the earlier you start, the easier and smoother things will go later on. Your future-self will thank you!
After each step in the eDNA data workflow, we propose a data checkpoint, with a list of questions/actions that must be carried out before the process moves to the next step. The intention is for one or more team members to take responsibility for carrying out each checkpoint. The same person can carry out all checkpoints, but this isn’t obligatory.
The process from sampling to output/publication is divided into six steps:
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Preparation: Ideally, before the project begins.
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Sample collection
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Lab analyses: The steps to go from sample to raw data.
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Bioinformatics: The steps to go from raw data to “operational data”, for example, an Operational Taxonomic Unit (OTU) table, and Amplicon Sequence Variant (ASV) table, or from droplets to eDNA concentrations. This step is specific for (e)DNA research and depends on the type of analysis, for example DDPCR versus metabarcoding.
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Data processing: The steps to go from “operational data” to an answer for a research question.
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Output/data publication: Make sure everything is correct and fully documented so that the results and output of the research are as valuable as possible.
After each step in the eDNA data workflow, we propose a data checkpoint, with a list of questions/actions that must be carried out before the process moves to the next step. The intention is for one or more team members to take responsibility for carrying out each checkpoint. The same person can carry out all checkpoints, but this isn’t obligatory.
The principles and practices described in this workflow are general in nature, continuously evolving, and developed in congruence with existing and emerging international network initiatives. These include, among others, eDNAqua-Plan, COST eDNA4Policy, COST DNABARDIV and the ECOSTAT (e)DNA Working Group advising under the Water Framework Directive.
Moreover, the work stems from a series of previous, or ongoing international projects including:
We welcome feedback and contributions from the community — if you notice gaps or opportunities for alignment with other initiatives, please do not hesitate to get in touch.
Next read: Checkpoints.