ArticleGenome biology2020
CHOP: haplotype-aware path indexing in population graphs.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Review
- A survey of sequence-to-graph mapping algorithms in the pangenome era.Genome biology · 2025Review
- Haplotype-aware sequence alignment to pangenome graphs.Genome research · 2024Article
- Co-linear chaining on pangenome graphs.Algorithms for molecular biology : AMB · 2024Article
- Review
- From the reference human genome to human pangenome: Premise, promise and challenge.Frontiers in genetics · 2022Article
- A variant selection framework for genome graphs.Bioinformatics (Oxford, England) · 2021Article
- Reference flow: reducing reference bias using multiple population genomes.Genome biology · 2021Article
- GraphAligner: rapid and versatile sequence-to-graph alignment.Genome biology · 2020Article
- Pangenome Graphs.Annual review of genomics and human genetics · 2020Review
- Assessing graph-based read mappers against a baseline approach highlights strengths and weaknesses of current methods.BMC genomics · 2020Article
- Haplotype-aware graph indexes.Bioinformatics (Oxford, England) · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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, bounding the search space to the number of haplotypes so that a combinatorial explosion is prevented. 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.