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Cited by 319Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalitiesGenome Rearrangement Algorithms

Genotyping structural variants in pangenome graphs using the vg toolkit

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Hickey, Glenn, Heller, David, Monlong, Jean, Sibbesen, Jonas A., Sirén, Jouni, Eizenga, Jordan, Dawson, Eric T., Garrison, Erik +2 more·2020·Genome Biology
DOI 10.1186/s13059-020-1941-7PMC PMC7017486

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Abstract

Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging SV catalogs for short-read SV genotyping experiments. We benchmark vg against state-of-the-art SV genotypers using three sequence-resolved SV catalogs generated by recent long-read sequencing studies. In addition, we use assemblies from 12 yeast strains to show that graphs constructed directly from aligned de novo assemblies improve genotyping compared to graphs built from intermediate SV catalogs in the VCF format.

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  • Alignments of such assemblies are essential for annotation and variant characterization.

    “Alignments of such assemblies are essential for annotation9 and variant characterization42 and should prove useful for reference-free pangenome construction of the variation present in a population43.”

    From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [42]

    The Results section (‘Graphs from alignment of de novo assemblies’; page unavailable) says whole-genome alignments of assemblies can reveal complex structural variation and support structural-variant genotyping. That supports the variant-characterization point attached to this citation, but the paper does not establish that such alignments are essential for variant characterization generally. The separate annotation claim is attached to another citation. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

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Cited by

Sorted by citations

Authors
Hickey, G., Heller, D., Monlong, J., Sibbesen, J. A., Sirén, J., Eizenga, J., Dawson, E. T., Garrison, E., Novak, A. M., & Paten, B.
Affiliations
  • University of California, Santa Cruz (US)
  • University of Cambridge (GB)
Corresponding author
Paten, Benedict
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2020-02-12
Volume
21
Issue
1
Pages
35-35
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-020-1941-7
PMC
PMC7017486
OpenAlex
W3007365321
Cited by
319
References
5
Citations by year
2026: 43 · 2025: 67 · 2024: 57 · 2023: 37 · 2022: 51 · 2021: 35 · 2020: 22 · 2019: 6
FWCI
11.71
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • eScholarship (California Digital Library) (submittedVersion, cc-by)
  • Apollo (University of Cambridge) (submittedVersion, cc-by)
  • Apollo (cc-by)
Funders
  • National Human Genome Research Institute (U54HG007990, U01HL137183, 2U41HG007234)
  • W. M. Keck Foundation (DT06172015)
  • Simons Foundation (SFLIFE# 35190)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
Keywords
structural variants, pangenome graphs, variation graphs, short-read sequencing, long-read sequencing, de novo assembly, yeast strain
MeSH terms
Whole Genome Sequencing, Saccharomyces cerevisiae, Software, Genome, Fungal, Genomic Structural Variation, Genotyping Techniques

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