Ultra-fast strain-level metagenomic profiling

Bacterial profiles from short-reads and across-sample strain-phylogenies per species

Latest release
A new database has been uploaded: protal-db-r226-0.5.1a.tar.gz, built from GTDB r226 marker genes. Protal version 0.6.0a is available via conda.

Preprint

Protal is described in our preprint on bioRxiv. Please cite it if you use protal in your work.

Protal: Ultra-fast metagenomic profiling and strain-resolved analysis. Joachim Fritscher, Anthony Duncan, Falk Hildebrand. doi: https://doi.org/10.64898/2026.08.03.742433

What is Protal?

Protal is a metagenomic profiling tool that allows for ultra-fast taxonomic profiling and strain-resolved analysis of bacterial communities from short-read sequencing data. It is designed to be efficient and user-friendly, enabling researchers to analyze large datasets quickly and accurately. Protal provides detailed bacterial profiles and across-sample strain-phylogenies per species, making it a powerful tool for microbial community analysis.

Figures

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Outline

Protal workflow: sequencing reads and the prebuilt GTDB flexmap go in; alignment, profiling and strain-level stages produce alignments, taxonomic profiles and per-species MSAs.

The protal workflow, from short reads to alignments, taxonomic profiles and per-species multiple sequence alignments.

Taxonomic Performance

Stacked bar chart counting how often each profiler performed significantly better than another, broken down by taxonomic rank. Protal ranks highest.

How often each profiler performed significantly better than another, across metrics, datasets and taxonomic ranks.

Strain-level Performance

Boxplots of multiple sequence alignment error rate, total errors and sensitivity for protal, protal-mini and StrainPhlAn 4.

Multiple sequence alignment quality against StrainPhlAn 4: fewer errors at comparable sensitivity.