MetaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.

ABSTRACT: Metagenomic approaches offer unprecedented opportunities to characterize microbial community structure and function, yet several challenges remain unresolved. Inconsistent genome quality impairs reliability of metagenome-assembled genomes, lack of unified taxonomic criteria limits cross-study comparability, and multi-step workflows involving numerous programs and parameters hinder reproducibility and accessibility. We benchmarked existing programs and parameters using simulated metagenomic data to identify optimal configurations. metaFun is an open-source, end-to-end pipeline that integrates quality control, taxonomic profiling, functional profiling, de novo assembly, binning, genome assessment, comparative genomic analysis, pangenome annotation, network analysis, and strain-level m

SUBMITTER: Lee HG 

PROVIDER: S-EPMC12818822 | biostudies-literature | 2026 Dec

REPOSITORIES: biostudies-literature