EGGS: Empirical Genotype Generalizer for Samples
T Quinn Smith, Amatur Rahman, Zachary A Szpiech · 2026
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Description
Geneticists simulate ancient populations by copying real genomes and letting the copies drift, but missing data in the real samples complicates the game. T Quinn Smith, Amatur Rahman, and Zachary Szpiech released a tool in 2026, called EGGS. It generalizes from a stretch of real genotypes, gaps included, and paints matching gap patterns onto simulated copies.
The tool can also strip phase and orientation from the data, fake ancient DNA damage and sequencing errors, and collapse samples into pseudo-haploid form. It converts between the field's common file formats and is written in C for speed. Code, executables, and a manual are posted openly on GitHub.
Catalog record
| CREATOR | T Quinn Smith, Amatur Rahman, Zachary A Szpiech |
|---|---|
| YEAR | 2026 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 16 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |