Frequently Asked Questions

What is QualiBact?

QualiBact is a community-driven framework for species-specific quality control of bacterial genome assemblies. We curate thresholds, visualizations, and reference datasets to help labs adopt consistent QC standards.

Who maintains the thresholds?

Thresholds are derived from the QualiBact pipeline (typically the qualibact-v1 scheme) and reviewed by the CGPS team plus community contributors. Each release lists the scheme version used for every species.

How often is QualiBact updated?

We update the dataset whenever we finish a new curation cycle—usually every few months, or sooner when large data contributions arrive. Check the Summary page or release notes for the most recent timestamp.

How do I request a new species?

See the Organism Requests page for the current queue and submission instructions. If your species is missing, email nabil_at_happykhan.com with relevant details so we can prioritize it.

Can I contribute my own thresholds or data?

Yes! The Contributing page outlines two workflows: submitting raw assembly metrics so we can run QualiBact, or sharing your own validated thresholds for inclusion. Contributors receive credit in releases and publications.

What formats do you support for downloads?

All tabular results are provided as CSV (often compressed as .csv.xz). Plots are PNG files. The Next.js app also includes manifests in JSON—such as refseq_metrics.json—to help downstream tooling discover assets.

Where can I report issues or bugs?

Open an issue on the QualiBact GitHub repository with as much context as possible (species, scheme, error logs). You can also email the maintainers if the problem involves sensitive data.