ArticleGenome research2024
Haplotype-aware sequence alignment to pangenome graphs.
Article in Genome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed.
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Haplotype-Resolved Genome Assemblies for Norwegian Red Cattle.Animal genetics · 2026Article
- Pangenome-based genome inference using integer programming.Genome research · 2025Article
- Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe.Research square · 2025Article
- Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe.bioRxiv : the preprint server for biology · 2025Article
- Panaln: indexing pangenome for read alignment.Bioinformatics (Oxford, England) · 2025Article
- Exploiting uniqueness: seed-chain-extend alignment on elastic founder graphs.Bioinformatics (Oxford, England) · 2025Article
- Review
- A survey of sequence-to-graph mapping algorithms in the pangenome era.Genome biology · 2025Review
- Complexity welcome: Pangenome graphs for comprehensive population genomics.Quantitative plant biology · 2025Review
- Integer programming framework for pangenome-based genome inference.bioRxiv : the preprint server for biology · 2024Article
- Co-linear chaining on pangenome graphs.Algorithms for molecular biology : AMB · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Modern pangenome graphs are built using haplotype-resolved genome assemblies. When mapping reads to a pangenome graph, prioritizing alignments that are consistent with the known haplotypes improves genotyping accuracy. However, the existing rigorous formulations for colinear chaining and alignment problems do not consider the haplotype paths in a pangenome graph. This often leads to spurious read alignments to those paths that are unlikely recombinations of the known haplotypes. In this paper, we develop novel formulations and algorithms for sequence-to-graph alignment and chaining problems. Inspired by the genotype imputation models, we assume that a query sequence is an imperfect mosaic of reference haplotypes. Accordingly, we introduce a recombination penalty in the scoring functions for each haplotype switch. First, we solve haplotype-aware sequence-to-graph alignment in [Formula: see text] time, where
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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.