BactFlow Provides Graphical Workflow for Bacterial Genome Assembly and Annotation

Bioinformaticians have developed BactFlow, an open-source interactive application designed to streamline bacterial single-isolate genome assembly and downstream characterization. As genomic reconstruction increasingly relies on short-read, long-read, and hybrid sequencing methodologies, coordinating sequence read processing, de novo assembly, quality checks, and functional evaluation across distinct data types has typically required substantial specialized bioinformatics expertise. The software addresses these operational bottlenecks by integrating the multi-stage analysis pipeline into a unified browser-based interface.

The platform accommodates several major sequencing technologies, providing direct support for Oxford Nanopore and Pacific Biosciences long reads, Illumina short reads, and hybrid combinations pairing Nanopore with Illumina datasets. Within its local web browser dashboard, the tool consolidates initial sequence read processing and quality assessment, primary genome assembly execution, and comprehensive post-assembly analysis alongside real-time run-status monitoring. This consolidated structure allows researchers to supervise every analytical phase without toggling between disconnected command-line scripts.

Beyond structural sequence assembly, BactFlow incorporates integrated downstream analytical modules to characterize reconstructed bacterial genomes. The application combines automated genome-quality assessment, taxonomic classification, gene annotation, and plasmid prediction, while also rendering interactive genome visualizations directly in the user interface. During performance demonstrations, the researchers evaluated four distinct assembly routes using publicly available Nanopore, Illumina, and PacBio datasets, as well as joint Nanopore-Illumina hybrid assembly workflows.

Designed for deployment on Linux environments, the tool can be initiated with a single terminal command using Conda, Docker, or Apptainer and Singularity containerization platforms. Following this initial environment setup, investigators configure and execute complex analytical workflows entirely through the graphical user interface, removing the necessity of manually executing separate bioinformatics packages. The integrated interface thereby standardizes single-isolate bacterial genomic analysis across varied sequencing methodologies.

The software development was led by researchers including Wenwen Li, Axel Soto-Serrano, Eoghan Thomas Reilly, Farhad M. Panah, and Lukasz Krych, who published the tool as an open-access software article in BMC Bioinformatics. To make the pipeline accessible for community inspection and local deployment, the authors deposited the source code in an open repository hosted on GitHub at https://github.com/farhadm1990/bactflow. By releasing the application as an open-source tool, the team enables researchers to inspect, download, and execute the analytical environment locally for single bacterial isolate characterization.

The workflow is structured to address the diverse practical requirements of bacterial genomics by unifying distinct sequencing formats within an interactive environment. Long-read datasets generated on Nanopore and PacBio instruments, as well as short-read Illumina collections, can be processed directly through their respective specialized assembly pathways or integrated into a Nanopore-Illumina hybrid assembly sequence. In addition to primary sequence assembly, the system coordinates downstream tasks including taxonomic classification, gene annotation, plasmid prediction, quality assessment, and run-status monitoring, providing a single operational platform for isolate evaluation.

Operational access follows initial deployment on a Linux platform using standard software package management or container systems, specifically Docker, Apptainer/Singularity, or Conda. Once launched through the single startup command, researchers control parameter configurations and run operations directly through the browser interface without executing separate terminal routines for each underlying program. This design consolidates read assessment, assembly pipelines, and post-assembly analysis across varying data types.

Subject of Research: BactFlow software for bacterial genome assembly and annotation

Article Title: BactFlow: a graphical workflow for bacterial genome assembly and annotation

Article References: Li, W., Soto-Serrano, A., Reilly, E. T., Panah, F. M., & Krych, L. (2026). BactFlow: a graphical workflow for bacterial genome assembly and annotation. BMC Bioinformatics. https://doi.org/10.1186/s12859-026-06767-8

Image Credits: AI Generated

DOI: 10.1186/s12859-026-06767-8

Keywords: BactFlow, bacterial genome assembly, genome annotation, bioinformatics workflow, long-read sequencing, short-read sequencing, hybrid assembly, Oxford Nanopore, PacBio, Illumina, plasmid prediction, taxonomic classification, genome quality assessment, Docker, Apptainer, Conda, interactive genome visualization