BactFlow: a graphical workflow for bacterial genome assembly and annotation
Year: 2026
Type: article
Abstract: 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.
Source: BMC Bioinformatics
Institution: University of Copenhagen
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,990
OpenAlex ID: W7225828556
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