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Caribou pipeline for the alignment-free bacterial identification and classification in metagenomics sequencing data using machine learning
| Description: | This dataset contains sequencing data used to train the models of the Caribou pipeline. We developed this pipeline for alignment-free bacterial identification and classification in metagenomics sequencing data using machine learning. The datasets were derived from the GTDB v.202 database (https://data.gtdb.ecogenomic.org/releases/release202/202.0/) and include training steps using the species representatives, as the benchmark datasets used non-representative whole genomes. We also simulated sequencing reads to evaluate and compare performance on whole genomes and sequencing reads. We provide models and encoding files of CNN-trained models; datasets used for training, validation and testing of models, randomly sampled from representative genomes; and datasets used for benchmarking the method against state-of-the-art methods, randomly sampled from non-representative whole genomes and simulated reads. |
| Notes: | This data was used in Nicolas de Montigny's Master's degree thesis (https://archipel.uqam.ca/18182/) |
| Authors: | de Montigny, Nicolas; University of Quebec at Montreal;  0000-0002-3708-4055Steven W., Kembel; University of Quebec at Montreal; 0000-0001-5224-0952Abdoulaye Baniré, Diallo; University of Quebec at Montreal |
| Keywords: | metagenomics alignment-free DNA classification classification models machine learning neural networks bacterial genomes taxonomic classification |
| Field of Research: | Computer and information sciences > Artificial intelligence (AI) > Machine learning
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| Publication Date: | 2024-12-12 |
| Publisher: | Federated Research Data Repository / dépôt fédéré de données de recherche |
| Funder: | Natural Sciences and Engineering Research Council of Canada (NSERC) |
| URI: | https://doi.org/10.20383/103.01160 |
| Related Identifiers: |
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Access to this dataset is subject to the following terms:
Creative Commons Attribution 4.0 International (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/
Citation
de Montigny, N., Steven W., K., Abdoulaye Baniré, D. (2024). Caribou pipeline for the alignment-free bacterial identification and classification in metagenomics sequencing data using machine learning. Federated Research Data Repository. https://doi.org/10.20383/103.01160
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