PT  - JOURNAL ARTICLE
AU  - Tom Mokveld
AU  - Jasper Linthorst
AU  - Zaid Al-Ars
AU  - Henne Holstege
AU  - Marcel Reinders
TI  - CHOP: Haplotype-aware path indexing in population graphs
AID  - 10.1101/305268
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 305268
4099  - http://biorxiv.org/content/early/2019/03/14/305268.short
4100  - http://biorxiv.org/content/early/2019/03/14/305268.full
AB  - The practical use of graph-based reference genomes depends on the ability to align reads to them. Performing substring queries to paths through these graphs lies at the core of this task. The combination of increasing pattern length and encoded variations inevitably leads to a combinatorial explosion of the search space. We propose CHOP a method that uses haplotype information to prevent this from happening. We show that CHOP can be applied to large and complex datasets, by applying it on a graph-based representation of the human genome encoding all 80 million variants reported by the 1000 Genomes project.