CHOP: Haplotype-aware path indexing in population graphs

Abstract excerpt

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 sh...

Topics

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• Algorithms
• Computer Graphics
• Genome, Human
• Genotyping Techniques
• High-Throughput Nucleotide Sequencing
• HLA Antigens
• Sequence Alignment
• Software

Identifiers and source

Literature Corpus work

3056dfa5-b8ec-5019-b529-7dc7441888c8

DOI

10.1101/305268