Warning
This repository is a prototype, the application has been fully rewritten from scratch here
Myrio is a command-line application designed to identify the taxonomy of a plant from a sample.
The name Myrio is inspired by the scientific name Myriophyllum spicatum, commonly known as Eurasian watermilfoil, an aquatic plant frequently found in the Léman.
If you are a contributor, please refer to this document.
- Extend the database to vascular plants (Tracheophyta) or even further if needed
- Complement the (BOLD) database with other sources (e.g. Genebank)
- Compress and make a release of the database(s) used (IMPORTANT: MUST BE LICENSED UNDER CC BY-NC-SA, ATTRIBUTION SHOULD BE ADDED TO THE HEADER LINE OF THE FASTA SEQUENCES WHERE IT IS REQUIERED, WE CANNOT USE THE DATABASE ITSELF FOR COMMERCIAL PURPOSES)
- License this codebase
- Implement BLASTN into the main cli-pipeline
- Implement a robust testing/scoring pipeline
- Use a ./bin/ solution for executables used
- Train a model to recognize the species instead of the genus
- Make a logo
- And much more ...
You'll need the following tools installed beforehand: uv, rust toolchain, seqkit
- Wei Shen, Botond Sipos, and Liuyang Zhao. 2024. SeqKit2: A Swiss Army Knife for Sequence and Alignment Processing. iMeta e191. doi:10.1002/imt2.191.
- raxtax: A k-mer-based non-Bayesian Taxonomic Classifier; Noah A. Wahl, Georgios Koutsovoulos, Ben Bettisworth, Alexandros Stamatakis; bioRxiv 2025.03.11.642618; doi: https://doi.org/10.1101/2025.03.11.642618
- Alexander J. Petri, Kristoffer Sahlin. De novo clustering of extensive long-read transcriptome datasets with isONclust3. bioRxiv 2024.10.29.620862; doi: https://doi.org/10.1101/2024.10.29.620862
- Ratnasingham, Sujeevan, and Paul D N Hebert. “bold: The Barcode of Life Data System (http://www.barcodinglife.org).” Molecular ecology notes vol. 7,3 (2007): 355-364. doi:10.1111/j.1471-8286.2007.01678.x