The design and construction of reference pangenome graphs

2020/03/13 by Heng Li, Li, Heng, Xiaowen Feng +3 · 10 citations
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Chromosomal and Genetic Variations #FOS: Biological sciences #Genome Rearrangement Algorithms #Genomics (q-bio.GN) #Genomics and Phylogenetic Studies

paper · pdf · doi:10.48550/arxiv.2003.06079

openalex publication_date 2020/03/13 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

Abstract

The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists remain an open challenge. Here we propose a graph-based data model and associated formats to represent multiple genomes while preserving the coordinate of the linear reference genome. We implemented our ideas in the minigraph toolkit and demonstrate that we can efficiently construct a pangenome graph and compactly encode tens of thousands of structural variants missing from the current reference genome.

Citations

• A framework for variation discovery and genotyping using next-generation DNA sequencing data
• Introducing difference recurrence relations for faster semi-global alignment of long sequences

Cited by

• An Allele-Centric Pan-Graph-Matrix Representation for Scalable Pangenome Analysis
• A Pan‐TE Map Reveals the Important Role of Transposable Elements in Gene Expression and Phenotypic Diversity in 2,311 Rapeseed Accessions
• High‐Quality Genome Assembly of Diplocarpon coronariae Unveils LTR Retrotransposon‐Driven Structural Dynamics in Fungi Evolution
• Billi: Provably Accurate and Scalable Bubble Detection in Pangenome Graphs
• The pangenome enhances the understanding of the genetic diversity of papaya
• On Deriving Synteny Blocks by Compacting Elements
• Haplotype-resolved diploid genome inference on pangenome graphs
• Pangenome-guided sequence assembly via binary optimisation
• SVPG: A pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples
• The reference-free pangenome of Arabidopsis thaliana

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