Find useful microhaplotypes, understand where they occur, and connect them to the breeding programs and people who can put them to work.
HapSearch is a web-based exploration platform for microhaplotype data in specialty crop breeding, hosted by Breeding Insight at hapsearch.breedinginsight.org. It brings marker sequences, variants, samples, projects, and collaborator information into one searchable interface.
Microhaplotypes are short genomic regions containing multiple nearby variants observed together. Their allelic diversity and local phase information make them useful for characterizing germplasm, tracking trait-associated variation, and designing crosses.
Microhaplotype data is often scattered across spreadsheets, local databases, and analysis scripts. HapSearch connects these sources so breeders and researchers can find the microhaplotypes, samples, and collaborators relevant to their work.
- Filter by Programs: browse breeding programs and projects, their PIs and institutions, and the microhaplotypes they hold
- Microhaplotypes: search by full Clone ID, chromosome, or sample, see which samples carry a microhaplotype, and save that sample list as CSV
- Multiple Sequence Alignment: view each microhaplotype aligned to its locus reference exactly as BIGr and BIGapp align it, with SNP and indel annotation
- Database Overview: summarize coverage across species, chromosomes, samples, and projects, and export microhaplotype accumulation and sharing curves as PNG, JPEG, or SVG
HapSearch is built with Python, Flask, Dash, Plotly, BioPython, and SQLite. Microhaplotype alignments are computed in R (Bioconductor pwalign) when the database is built.
All data lives in one SQLite file built by scripts/build_database.py from the species data repositories listed in data_sources.toml, such as alfalfa_haplotype_db. To publish new data, see:
Run the automated tests with pytest.
HapSearch is released under the Apache License 2.0.