The EggNOG script is a command-line tool that automates the use of eggNOG-mapper, a high-throughput functional annotation tool based on orthology assignments from the eggNOG database. eggNOG-mapper allows researchers to functionally annotate protein, transcript, genome, or metagenome sequences with high accuracy, avoiding false positives from close paralogs by focusing on fine-grained orthologs. This script simplifies the process by handling all preparatory steps: it checks and downloads required core databases (like eggnog.db) and the DIAMOND protein database, ensures the environment is properly set up, and executes the emapper.py pipeline using user-defined parameters. The script takes four inputs—an input FASTA file, an output directory, the number of CPUs, and the sequence type (proteins, CDS, genome, or metagenome)—and outputs a cleaned annotation.tsv table with meaningful gene annotations. This automation makes eggNOG-mapper easier to integrate into large-scale genome or transcriptome annotation workflows.