README.md

YADeNA

Yet Another De Novo Assembler

Contributing

1. Fork and clone the repository
2. Do your changes
3. Install conda
4. Add bioconda channel:

   conda config --add channels defaults
   conda config --add channels bioconda
   conda config --add channels conda-forge
   conda config --set channel_priority strict
   

5. Create conda environment and install dependencies from the environment.yml file:

   conda env create -n YADeNA -f environment.yml
   

6. Extract out_dir.zip into test_data/ OR
   1. Put FASTA file with reference genome into test_data/ directory
   2. Install ART
   3. Run simulate_data.sh
7. Activate the environment:

   conda activate YADeNA
   

8. Make your changes and, if necessary, install or remove packages using conda
9. Test the program:

   python test_assembler.py
   

   Or run it directly with necessary arguments:

   python assembler.py ...
   

10. Before committing, if you installed or removed packages, run the command

    conda env export > environment.yml
    

11. Commit, push and do a pull request