Qiime2 classifiers (rbcl, Mollusc 18s) for testing the validity of using eDNA for carbon origin analysis from sediment cores

Qiime2 formatted classifiers that were created for a Natural England funded project by researchers at the James Hutton Institute. The pilot project aims to test the validity of using eDNA for carbon origin analysis from sediment cores. These classifiers for the rbcl and 18 Mollusc genes were made using RESCRIPt and Qiime2. 

The scripts used to created these classifiers are available at the James Hutton ICS GitHub blue-carbon-db . The files are as follows:

mollusc-espineira-classifier.qza is a classifer built from ncbi 18s Mollusc sequences, trained on the primer set from Espiñeira et al (2009).

rbcl-vasselon-zimmerman-F3-R1-classifier.qza is a classifer built from ncbi rbcl sequences, trained on the F3 and R1 primer set fromVasselon et al (2017).

Important: If you use these classifiers please be aware of the process used to create them and be sure to review the methods. These databases were created by downloading data from the NCBI in October 2023, sequence data available at the NCBI changes over time. To create the most up to date database a fresh download and re-evaluations of the databases would be preferable. All method and scripts can be found at blue-carbon-db 

If you use these database please reference this repository along with RESCRIPt and Qiime2 

Espiñeira, M., González-Lavín, N., Vieites, J. M. and Santaclara, F. J. 2009 Development of a method for the genetic identification of commercial bivalve species based on mitochondrial 18S rRNA sequences. J Agric Food Chem, 28, 495-502 https://doi.org/10.1021/jf802787d

Vasselon, V., Rimet, F., Tapolczai, K. and Bouchez, A. 2017. Assessing ecological status with diatoms DNA metabarcoding: Scaling-up on a WFD monitoring network (Mayotte island, France). Ecological Indicators, 82, 1-12 https://doi.org/10.1016/j.ecolind.2017.06.024