Genotyping structural variants in pangenome graphs using the vg toolkit.


: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.


Genome Biol


Genome biology


Hickey G,Heller D,Monlong J,Sibbesen JA,Sirén J,Eizenga J,Dawson ET,Garrison E,Novak AM,Paten B




Has Abstract


2020-02-12 00:00:00














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    journal_title:Genome biology



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    journal_title:Genome biology

    pub_type: 杂志文章


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    journal_title:Genome biology

    pub_type: 杂志文章


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    journal_title:Genome biology

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    pub_type: 杂志文章


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    pub_type: 杂志文章


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    journal_title:Genome biology

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    journal_title:Genome biology

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    pub_type: 杂志文章


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    journal_title:Genome biology



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    journal_title:Genome biology

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    journal_title:Genome biology

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    journal_title:Genome biology

    pub_type: 杂志文章


    authors: de la Rica L,Rodríguez-Ubreva J,García M,Islam AB,Urquiza JM,Hernando H,Christensen J,Helin K,Gómez-Vaquero C,Ballestar E

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    journal_title:Genome biology

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    journal_title:Genome biology

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    authors: Suzuki A,Matsushima K,Makinoshima H,Sugano S,Kohno T,Tsuchihara K,Suzuki Y

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    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Lin C,Todo T

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    journal_title:Genome biology

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    authors: Joung JK,Voytas DF,Kamens J

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    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Haibe-Kains B,Desmedt C,Rothé F,Piccart M,Sotiriou C,Bontempi G

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    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Liang S,Tippens ND,Zhou Y,Mort M,Stenson PD,Cooper DN,Yu H

    更新日期:2017-01-18 00:00:00

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    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Lun ATL,Riesenfeld S,Andrews T,Dao TP,Gomes T,participants in the 1st Human Cell Atlas Jamboree.,Marioni JC

    更新日期:2019-03-22 00:00:00

  • The telosome/shelterin complex and its functions.

    abstract::The telomeres that cap the ends of eukaryotic chromosomes serve a dual role in protecting the chromosome ends and in intracellular signaling for regulating cell proliferation. A complex of six telomere-associated proteins has been identified--the telosome or shelterin complex--that is crucial for both the maintenance ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Xin H,Liu D,Songyang Z

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    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Walhout AJ

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    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Ruotolo R,Marchini G,Ottonello S

    更新日期:2008-04-07 00:00:00