BioFlux: A Suite of Automated Workflows for Bacterial and Fungal Whole-Genome Sequencing Analysis

BioFlux is a suite of automated and reproducible Snakemake workflows for bacterial and fungal whole-genome sequencing (WGS) analysis. It includes BacFlux for Illumina short reads, BacFluxL for Oxford Nanopore long reads, and BacFluxL+ for hybrid datasets, each integrating modules for quality control, assembly, annotation, assessment of completeness and contamination, secondary metabolite prediction, antimicrobial resistance and virulence gene screening, and plasmid or phage detection. FunFlux extends this framework to fungal genomes. Together, these pipelines provide standardized, scalable solutions for microbial genomics, reducing manual effort and ensuring reproducibility across sequencing platforms and organism types. Built with continuous feedback from researchers, BioFlux now enables scientists to concentrate on biological insights rather than technical complexity.