Easy and interactive taxonomic profiling with Metabuli App

Abstract Summary Accurate metagenomic taxonomic profiling is critical for understanding microbial communities. However, computational analysis often requires command-line proficiency and high-performance computing resources. To lower these barriers, we developed Metabuli App, an all-in-one desktop application that efficiently runs taxonomic profiling locally on a consumer-grade computer. It features user-friendly graphical interfaces for custom database curation, raw read quality control (QC), taxonomic profiling, and interactive result visualization. Availability and implementation GPLv3-licensed source code and prebuilt apps for Windows, macOS, and Linux are available at https://github.com/steineggerlab/Metabuli-App and are archived at https://doi.org/10.5281/zenodo.15876171. Analysis scripts are available at https://github.com/jaebeom-kim/metabuli-app-analysis. The Sankey-based taxonomy visualization component is available at https://github.com/steineggerlab/taxoview for easy integration into other web projects. Contact martin.steinegger{at}snu.ac.kr Competing Interest Statement M.S. acknowledges outside interest in Stylus Medicine. The remaining authors declare no competing interests. Footnotes App updates (v1.1.1): Added multi-sample processing with fastp/fastplong QC, improved documentation, enhanced the Sankey visualization for publication-ready figures, and boosted Windows performance. Manuscript changes: Described these enhancements; expanded comparisons with MG-RAST, Galaxy, and MGnify; condensed Methods to emphasize Results; added new benchmarks of classification times across thread/RAM setups; and strengthened Conclusions with practical use cases.