BacAtlas

A locus-centred atlas of bacterial pangenomes.

⚠ This release reserves the name. It ships no pipeline and no data. The work is real and in progress; this package exists so that what is published later is published under the name the project is already called. Watch github.com/abelsond-cam/bacatlas.

What it is

A bacterial pangenome is usually presented around one reference genome, with everything else hung off it. That works until the interesting thing is a gene the reference does not have.

BacAtlas presents the pangenome as loci instead. A locus is a position in the genome, and what fills it: the structurally homologous genes found there across a species — however far their sequences have diverged — together with how consistently each neighbouring position is occupied. You search for a gene, and you get the neighbourhood it lives in.

Two genes that occupy the same position and are homologous in structure are syntelogs. Homology here means similar structure, inferred from protein-language-model embeddings, not sequence identity: syntelogs routinely differ far more in sequence than any identity threshold would group. That is the whole point — an identity threshold cannot see a conserved role filled by a divergent gene, and those are the genes that carry resistance and virulence.

How it is built

BacAtlas is the atlas; Nuna is the clustering method inside it.

Status

Early. The method clears its correctness gate on Escherichia coli and Klebsiella pneumoniae, and a browser over both is running. Reproducibility against Panaroo, and the scale-up beyond the probe cohort, are in progress. Nothing here is peer-reviewed yet — treat it as a working draft.

Licence

BSD 3-Clause. © 2026 David Abelson.