ArticleNature methods2019
Long-read sequence and assembly of segmental duplications.
Article in Nature methods, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 papers.
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Who cites it
146 citing papers in PubMed.
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- Personalized reference genome-based pipeline reveals comprehensive haplotype-resolved views of cancer genomes.bioRxiv : the preprint server for biology · 2026Article
- Complete chromosome 21 centromere sequencing of families with Down syndrome.American journal of human genetics · 2026Article
- Genomes From 117 Vertebrate Species Reveal Rapidly Evolving Segmental-Duplication Landscapes.Genome biology and evolution · 2026Article
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- A global map for introgressed structural variation and selection in humans.Science (New York, N.Y.) · 2026Article
- Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.Nature communications · 2026Article
- Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion.Nature communications · 2026Article
- The diploid reference genome of a human embryonic stem cell line.bioRxiv : the preprint server for biology · 2026Article
- Donor-specific assemblies enhance somatic structural variant detection in complex genomic regions.bioRxiv : the preprint server for biology · 2026Article
- Impact of Tau overexpression on DNA replication dynamics in centromeres of human neural progenitor cells.iScience · 2026Article
- Higher order repeat structures reflect diverging evolutionary paths in maize centromeres and knobs.Genome biology · 2026Article
- A global view of human centromere variation and evolution.bioRxiv : the preprint server for biology · 2025Article
- Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.bioRxiv : the preprint server for biology · 2025Article
86 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
Abstract
We have developed a computational method based on polyploid phasing of long sequence reads to resolve collapsed regions of segmental duplications within genome assemblies. Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA ) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of long reads corresponding to distinct paralogs. We apply it to single-molecule, real-time sequence data from three human genomes and recover 33-79 megabase pairs (Mb) of duplications in which approximately half of the loci are diverged (<99.8%) compared to the reference genome. We show that the corresponding sequence is highly accurate (>99.9%) and that the diverged sequence corresponds to copy-number-variable paralogs that are absent from the human reference genome. Our method can be applied to other complex genomes to resolve the last gene-rich gaps, improve duplicate gene annotation, and better understand copy-number-variant genetic diversity at the base-pair level.
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