BactFlow: a graphical workflow for bacterial genome assembly and annotation

Bacterial genome reconstruction increasingly uses short-read, long-read, and hybrid sequencing strategies. However, coordinating read processing, genome assembly, quality assessment, and downstream characterization across these data types can require substantial bioinformatics expertise. We developed BactFlow ( https://github.com/farhadm1990/bactflow ), an open-source interactive app for bacterial single isolate genome assembly and downstream analysis. It supports Nanopore and PacBio long reads, Illumina short reads, and Nanopore-Illumina data for hybrid assembly. A single local browser interface integrates read processing and quality assessment, genome assembly, and post-assembly analysis, with run-status monitoring. BactFlow combines genome-quality assessment, taxonomic classification, gene annotation, plasmid prediction, and interactive genome visualization. We demonstrated four assembly routes using publicly available Nanopore, Illumina, and PacBio datasets, as well as Nanopore-Illumina hybrid assembly. After initial setup on Linux, BactFlow can be launched with a single command line using Docker, Apptainer/Singularity, or Conda. Users can then configure and run analyses through the user interface (UI) without manually invoking each bioinformatics tool. The integrated interface supports bacterial isolate genome analysis across multiple sequencing strategies.