OBIS Data challenge eDNA
The MARCO-BOLO project, a Horizon Europe funded project, is aiming to strengthen European marine, coastal and freshwater biodiversity observation to understand and restore ocean health. One of its goals is to validate environmental DNA (eDNA) based approaches for the monitoring of marine biodiversity. There is currently considerable variation in the analysis of eDNA data using bioinformatic pipelines. There is also no clear assessment of how these different pipelines and parameter choices therein affect the calculation of indicators. The WP2 and WP5 of MARCO-BOLO are testing different existing bioinformatic pipelines to develop recommendations and optimise the indicator workflows to report on biodiversity to the European Marine Strategic Framework Directive (MSFD).
Within WP2, OBIS is leading efforts together with UiT and VLIZ in organising an eDNA Data Analysis Challenge. The aim of the challenge is to compare the different bioinformatic pipelines currently used for eDNA analysis across the eDNA community. To include a large panel of pipelines in the comparison representative of the many pipelines being used, all eDNA researchers and practitioners with experience in analysing metabarcoding datasets are invited to participate. Upon registration, participants can select the datasets they would like to analyse, choosing between an 18S plankton time series, and a set of 12S, 16S and COI aquarium samples targeting fish. Next, participants apply their own - or their favourite - pipeline to process the raw eDNA datasets into ASV/OTU and taxonomy tables.
After sending in their resulting tables, the challenge team will collect, compile and compare the results across the many participants and pipelines they decided on using. These results will allow us to finetune recommendations to guide user’s choice in bioinformatic pipelines. Furthermore, the results will allow us to test the pelagic habitat indicator workflows that are being developed by WP5 and evaluate how parameter choice affects the resulting biodiversity indicators.
The high number of participants and the numerous pipelines reflect the wide panel of tools that currently exist and the pressing need to assess the effects the analysis choices have on our capacity to inform on biodiversity monitoring.
Timeline of challenge
- Extended until the 13th of September 2024: Registration deadline. Datasets are shared with participants who expressed their interest to join.
- 30th of September 2024: Deadline for the submission of analysis results.
- 7th and 8th of October: Data comparison and indicator workflow development by MARCO-BOLO internally.
- Early November: MARCO-BOLO initial report.
Interested in participating?
eDNA practitioners interested in participating can still register their interest in the registration form.
All additional information and associated data files can be found on the dedicated GitHub page.
A first information session will be held online next Monday, September 9th at 15:00 CEST, to launch the start of the challenge and answer any questions participants might have.
