This is a Python script that calculates the Average Nucleotide Identity by Orthology (OrthoANI) (Lee et al., 2016).
If you need to download FASTA files from NCBI, you can retrieve them using the GenBank ID reference with this script. Detailed instructions are available in the Download_fasta_NCBI.
Reference
Imchang Lee, Yeong Ouk Kim, Sang-Cheol Park and Jongsik Chun. OrthoANI: An improved algorithm and software for calculating average nucleotide identity (2016). International Journal of Systematic and Evolutionary Microbiology. doi:10.1099/ijsem.0.000760. PMID:26585518.
Requirements
This Python script uses the OrthoANI CLI tool. To install it in your environment, run:
pip install orthoani
For more details, refer to the OrthoANI CLI documentation.
Setup
Download the script from here and grant execuation permissions:
chmod +x orthoani_CLI.py
Usage Example
Run the script with:
python orthoani_CLI.py <input_path_reference> <input_path_query> <output_folder> [output_file]
Example Command:
python orthoani_CLI.py dir/fasta_reference/ dir/fasta_query/ dir/orthoani_output orthoani_results.txt
Example Input Directories: <input_path_reference>:
ls dir/fasta_reference
NC_029066.1.fasta
NC_002484.2.fasta
NC_030929.1.fasta
<input_path_query>
ls dir/fasta_query
vContig1
Output:
The results will be saved in the specified output folder (e.g., orthoani_output) as a tab-delimited text file with three columns: reference, query, and ANI percentage.
Example Output:
cat /dir/orthoani_output/orthoani_results.txt
NC_029066.1.fasta vContig1.fasta 0.0
NC_002484.2.fasta vContig1.fasta 58.955
NC_030929.1.fasta vContig1.fasta 0.0