IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-47562-4.html
   My bibliography  Save this article

KSNP: a fast de Bruijn graph-based haplotyping tool approaching data-in time cost

Author

Listed:
  • Qian Zhou

    (PengCheng Laboratory)

  • Fahu Ji

    (Harbin Institute of Technology)

  • Dongxiao Lin

    (Shenzhen University)

  • Xianming Liu

    (PengCheng Laboratory
    Harbin Institute of Technology)

  • Zexuan Zhu

    (Shenzhen University
    Shenzhen University)

  • Jue Ruan

    (Chinese Academy of Agricultural Sciences)

Abstract

Long reads that cover more variants per read raise opportunities for accurate haplotype construction, whereas the genotype errors of single nucleotide polymorphisms pose great computational challenges for haplotyping tools. Here we introduce KSNP, an efficient haplotype construction tool based on the de Bruijn graph (DBG). KSNP leverages the ability of DBG in handling high-throughput erroneous reads to tackle the challenges. Compared to other notable tools in this field, KSNP achieves at least 5-fold speedup while producing comparable haplotype results. The time required for assembling human haplotypes is reduced to nearly the data-in time.

Suggested Citation

  • Qian Zhou & Fahu Ji & Dongxiao Lin & Xianming Liu & Zexuan Zhu & Jue Ruan, 2024. "KSNP: a fast de Bruijn graph-based haplotyping tool approaching data-in time cost," Nature Communications, Nature, vol. 15(1), pages 1-7, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47562-4
    DOI: 10.1038/s41467-024-47562-4
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-47562-4
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-47562-4?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Peter Edge & Vikas Bansal, 2019. "Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    2. Shilpa Garg, 2023. "Towards routine chromosome-scale haplotype-resolved reconstruction in cancer genomics," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Cheng-Kai Shiau & Lina Lu & Rachel Kieser & Kazutaka Fukumura & Timothy Pan & Hsiao-Yun Lin & Jie Yang & Eric L. Tong & GaHyun Lee & Yuanqing Yan & Jason T. Huse & Ruli Gao, 2023. "High throughput single cell long-read sequencing analyses of same-cell genotypes and phenotypes in human tumors," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    2. M. Mahmoud & Y. Huang & K. Garimella & P. A. Audano & W. Wan & N. Prasad & R. E. Handsaker & S. Hall & A. Pionzio & M. C. Schatz & M. E. Talkowski & E. E. Eichler & S. E. Levy & F. J. Sedlazeck, 2024. "Utility of long-read sequencing for All of Us," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    3. Anna Zimmermann & Julian E. Prieto-Vivas & Charlotte Cautereels & Anton Gorkovskiy & Jan Steensels & Yves Peer & Kevin J. Verstrepen, 2023. "A Cas3-base editing tool for targetable in vivo mutagenesis," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    4. Charlotte Cautereels & Jolien Smets & Peter Bircham & Dries De Ruysscher & Anna Zimmermann & Peter De Rijk & Jan Steensels & Anton Gorkovskiy & Joleen Masschelein & Kevin J. Verstrepen, 2024. "Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    5. Sina Majidian & Mohammad Hossein Kahaei & Dick de Ridder, 2020. "Minimum error correction-based haplotype assembly: Considerations for long read data," PLOS ONE, Public Library of Science, vol. 15(6), pages 1-12, June.
    6. Leanne M. Brown & Ryan A. Hagenson & Tilen Koklič & Iztok Urbančič & Lu Qiao & Janez Strancar & Jason M. Sheltzer, 2024. "An elevated rate of whole-genome duplications in cancers from Black patients," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    7. Can Luo & Yichen Henry Liu & Xin Maizie Zhou, 2024. "VolcanoSV enables accurate and robust structural variant calling in diploid genomes from single-molecule long read sequencing," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    8. Xiao Luo & Xiongbin Kang & Alexander Schönhuth, 2022. "VeChat: correcting errors in long reads using variation graphs," Nature Communications, Nature, vol. 13(1), pages 1-12, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47562-4. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.