Graph Genome Evaluation: Comparing Linear and Pangenome References for Structural Variant Detection
Does your reference genome affect structural variant detection?
This project benchmarks SV detection across three reference strategies:
| Strategy | Reference | Type |
|---|---|---|
| Linear | GRCh38 | Standard linear |
| Complete | T2T-CHM13 v2.0 | Telomere-to-telomere |
| Pangenome graph | HPRC v1.1 (Minigraph-Cactus) | Graph-based |
Evaluated on both short-read (Illumina WGS) and long-read (PacBio HiFi) data from clinical cohort.
Status: actively in development — results and scripts are updated as analysis completes.
Supervisor: Jesper Eisfeldt
Subject reader: Adam Ameur
The project is released under the GPL-3.0 license.