Genome ANI Calculator

Overview

The Genome ANI Calculator is a Python script that calculates the Average Nucleotide Identity (ANI) based on genomes of a pair of prokaryotes. It utilizes BLAST tools for sequence alignment.

Features

• Splits genome sequences into segments (1,020 bp) for analysis
• Creates and uses BLAST databases for efficient comparisons
• Calculates ANI for pairwise genome comparisons
• Generates an ANI tables as a result

Requirements

• Python 3.x
• BioPython library
• BLAST tools (makeblastdb, blastn)

'Preprocessing Steps"

1. First, keep all genomes in one directory.
2. If file names contain spaces, run remove_spaces.py to replace spaces with underscores (_) in file names.
3. Then run the command as given below.

Usage

python ANI_calculator.py --genomes-dir <path/to/genomes> --output-dir <output/directory> --formatdb-executable <path/to/makeblastdb> --blastall-executable <path/to/blastn> --num_threads <number_of_threads> --clean

Options:
--genomes-dir: Directory containing genome sequences in FASTA format.
--output-dir: Output directory for the results.
--formatdb-executable: Path to the makeblastdb executable.
--blastall-executable: Path to the blastn executable.
--num_threads: Specify the number of threads used by BLAST (default is 3).
--clean: Remove redundant files created during the analysis.


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https://github.com/MdUmar-tech/Diagonal_Heatmap_dendrogram