QualiBact — Community-agreed bacterial genome assembly quality thresholds

What is QualiBact?

QualiBact is a repository of community-agreed thresholds for assessing the quality of bacterial genome assemblies. We evaluate genomes using a set of standard metrics to help researchers identify high-quality assemblies for downstream analyses. The thresholds described here are implemented in SpecCheck. Source code for this website is available at QualiBact.

We have developed an automated and consistent process for defining thresholds, qualibact-engine. This is the default method applied for many species. For a full description see the methods page for qualibact-v1 (/methods/qualibact-v1). The source code for the engine is available at QualiBact-engine.

The repository also includes manually curated thresholds for certain species where the automated approach was insufficient.

What QualiBact is NOT

  • A universal definition of genome quality
  • A replacement for manual curation in special cases
  • Tailored to long-read assemblies (though GC and genome size thresholds still apply)
  • A strict pass/fail system — thresholds are intended as guidance, not biological absolutes

Quick Start: How to Use QualiBact

  1. Find your species on the species list.
  2. Review the thresholds and summary metrics for your organism.
  3. Apply thresholds using SpecCheck or in your own analysis pipeline.
  4. Request new species or improvements via the Requests page.

Who is QualiBact for?

  • Public-health laboratories performing routine bacterial genomics
  • Researchers analysing genomic diversity, AMR, or phylogeny
  • Bioinformatics pipeline developers
  • Benchmarking and validation studies
  • Anyone who needs a consistent, species-aware QC framework

Citation

If you use QualiBact, please cite the following:

Alikhan, NF. Species specific quality control of bacterial de novo genome assemblies using QualiBact. Available at: https://github.com/happykhan/qualibact (Accessed: [insert date]).

There maybe additional citations for specific methods used, which will be mentioned on the relevant QC scheme pages.