AT-GC

Accurate Taxonomic Genomic Computer

This research is about classifying microbes into phyla by genomic signatures using machine learning

Usage

• To run this program start you can start by downloading the repo manually or cloning it using the your favorite terminal and the git tool:

git clone https://github.com/URI-Bioinformatics/AT-GC.git

• The next step is to set up your python environment to be able to run the code. We do so by installing the required packages found on requirements.txt

cd AT-GC
pip install -r requirements.txt

• Next, make sure you download your data and make sure the data is organized as such:

Data/
├──Cyanobacteriota/
|   |── assembly_data_report.jsonl
|   ├──── dataset_catalog.json
|   ├──── data_summary.tsv
|   ├──── GCF_000011345.1
|   |     └── GCF_000011345.1_ASM1134v1_genomic.fna
|   ├──── GCF_000011385.1
|   |     └── GCF_000011385.1_ASM1138v1_genomic.fna
|   |     .
|   |     .
|   |     .
├──Fusobacteriota/
|   |── assembly_data_report.jsonl
|   ├──── dataset_catalog.json
|   ├──── data_summary.tsv
|   ├──── GCF_000011355.1
|   |     └── GCF_000011355.1_ASM1134v1_genomic.fna

• Run the program passing the path to the data folder (full or relative as an argument

python model_script.py /path/to/data/folder

• Finally, results can be found in results_summary.txt and individual validation graphs can be found in individual k-mers folders results_k{k}