Arche: An Advanced Flexible Tool for High-Throughput Annotation of Functions on Microbial Contigs

Abstract

The growing volume of microbial genomic data has increased the need for annotation tools that are both comprehensive and accessible. However, existing pipelines often present substantial limitations: some are constrained to a single database or search algorithm, others require complex installations, or high computational resources. Arche is a command-line annotation pipeline designed to overcome these challenges by integrating a flexible and hierarchical workflow that combines multiple search strategies (BLAST, DIAMOND, HMMER3) and databases (UniProtKB, KOfam, TIGRFAMs, NCBIFAMs, and Pfam). Arche supports the annotation of prokaryotic genomes and metagenomes, and it produces detailed functional tables including enzyme commission (E.C.) numbers, KEGG and eggNOG orthologous identifiers, gene names, and protein descriptions. Benchmarking against widely used tools such as Prokka, Bakta, RAST, MicrobeAnnotator, and eggNOGmapper shows that Arche retrieves a higher number of functional identifiers per gene in many cases. By offering modularity, compatibility with standard desktop systems, and more manageable database requirements than other high-throughput tools, Arche provides a practical and robust solution for functional annotation in genomic and metagenomic studies.