Tools, workflows, and reproducible project resources created to solve practical problems in pangenomics and comparative genomics.
Open tools / 01
Each repository connects to a concrete research need: association on genome graphs, analysis of complex polyploids, or readable multi-genome synteny.
A graph-node-based workflow for sensitive association analysis across diploid and polyploid species. It counts node support from graph alignments, builds marker tables, and maps significant nodes back to linear coordinates.
Analysis resources for the polyploid-aware Saccharum pangenome project, organized around chromosome communities, allele variation, homoeolog ecosystems, multi-omics, population genomics, GWAS, and benchmarking.
An R-driven workflow that extracts target regions, aligns sequences, and draws synteny across multiple genomes, with optional phylogenetic-tree integration for comparative interpretation.
Development principles / 02
The goal is not software for its own sake. A useful research tool makes an analysis more transparent, repeatable, and open to scrutiny.
Start from a biological limitation that existing methods cannot represent or test well.
Use simulations, benchmarks, and interpretable examples to define when a method is reliable.
Publish code, parameters, and project structure so others can reproduce and extend the analysis.