pommevilla / sbfp

biofilm bioinformatics feature-selection kmer-counting machine-learning population-structure salmonella snakemake xgboost

Salmonella biofilm formation prediction

Workflow DAG

Running the pipeline

Edit the config file in the indicated places
Install snakemake. A bare conda/mamba environment is recommended (ie., created with mamba craete -c conda-forge -c bioconda -n snakemake snakemake)
Run the pipeline with snakemake --use-conda -c

To Dos

Feature selection
Add tree building to pipeline

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biofilm bioinformatics feature-selection kmer-counting machine-learning population-structure salmonella snakemake xgboost

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