SCARAP: scalable cross-species comparative genomics of prokaryotes
Stijn Wittouck, Tom Eilers, Vera van Noort, Sarah Lebeer · 2025
Read SCARAP: scalable cross-species comparative genomics of prokaryotes by Stijn Wittouck, Tom Eilers, Vera van Noort, Sarah Lebeer (2025) in the Tower of Babel, a free online library of public-domain works preserved in clean, searchable text. No sign-up. The full text is served as a plain-text file at a predictable URL, where text is present: https://antarctic-labs.com/tower-of-babel/pmc-11681940.txt.
Description
Stijn Wittouck and co-authors build a faster engine for comparing bacterial genomes across species in a 2024 paper. Comparative genomics leans on two chores: grouping genes into families across many genomes, the pangenome, and extracting the core set nearly every genome shares. Species-level tools run fast, but broader datasets bog down, and breadth is where evolution gets interesting.
Their toolkit, SCARAP, packs three modules: a pangenome builder, a direct core-genome extractor that skips building the full pangenome first, and a sampler that picks representative genomes. Benchmarks show the pangenome module running up to ten times faster than rivals at matching accuracy. The sampler proved itself on over thirty-one thousand genomes of one bacterial order, distilling a representative set. A final analysis of gene fixation frequency revealed that common-but-never-fixed genes often serve bacteriophages, the viruses of bacteria.
Catalog record
| CREATOR | Stijn Wittouck, Tom Eilers, Vera van Noort, Sarah Lebeer |
|---|---|
| YEAR | 2025 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 36 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |