This repository contains the code and data used for the benchmark study on fish marker family assignment, as described in the paper "Transductive learning from a transformer foundation model improves the taxonomic classification of eDNA metabarcodes".
For this study, we utilized the MIDORI2 Reference and MitoFish databases. Teleo, Mifish, Berry and Ac16 markers extraction was performed using the CRABS tool via Docker execution (details provided in data/README.md)
Detailed information about the requirements and execution of each script is available in their respective directories under scripts/.
All methods were tested on a Linux operating system. For use on other platforms, please refer to the original documentation provided by the authors (links below).
- OBITOOLS 4 ( code)
- MMSEQS2 (code/paper)
- BERTAX (code/paper)
- BouillaBert (code/paper)
- DNAGPT (code/paper )
To enable figure reproduction, the prediction CSV file is provided along with the corresponding scripts script.