CHOP: haplotype-aware path indexing in population graphs.
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ABSTRACT:
SUBMITTER: Mokveld T
PROVIDER: S-EPMC7066762 | biostudies-literature | 2020 Mar
REPOSITORIES: biostudies-literature
Publications
CHOP: haplotype-aware path indexing in population graphs.
Mokveld Tom T Linthorst Jasper J Al-Ars Zaid Z Holstege Henne H Reinders Marcel M
Genome biology 20200311 1
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. Instead of heuristic filtering or pruning steps to reduce the complexity, we propose CHOP, a method that constrains the search space by exploiting haplotype information, boundin ...[more]
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