annoSnake: A Snakemake Workflow for Taxonomic and Functional Annotation of Metagenomes and Metagenome-Assembled Genomes

Abstract Omic technologies revolutionised research in microbiomics and helped decipher the complex community structure of gut microbiota, each comprising hundreds of species of bacteria, archaea, and protists. Even as sequencing costs decrease, understanding these communities remains a challenge. Here, we introduce annoSnake, a Snakemake workflow that facilitates taxonomic and functional annotation of metagenomes and metagenomic-assembled genomes (MAGs). This user-friendly and highly flexible workflow integrates state-of-the-art software packages, taking raw sequencing reads, assembling them into contigs, assigning taxonomies and annotating them using various popular protein databases. The workflow handles paired-end as well as interleaved read data, and provides publication-ready figures and tables for downstream analysis. annoSnake, as all Snakemake workflows, is highly scalable, reproducible, and portable, enabling execution across diverse high-performance computing environments with remarkable efficiency.