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Read Clouds Uncover Variation in Complex Regions of the Human Genome

  • Alex BisharaEmail author
  • Yuling Liu
  • Dorna Kashef-Haghighi
  • Ziming Weng
  • Daniel E. Newburger
  • Robert West
  • Arend Sidow
  • Serafim Batzoglou
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9029)

Abstract

The rapid advance of next-generation sequencing (NGS) technologies has decreased the cost of genomic sequencing dramatically, enabling accurate variant discovery across whole genomes of many individuals. Current large-scale and cost-effective resequencing platforms produce reads of limited length, and as a result, reliable identification of variants within highly homologous regions of a target genome remains challenging.

References

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    Abecasis, G.R., Auton, A., Brooks, L.D., DePristo, M.A., Durbin, R.M., Handsaker, R.E., Kang, H.M., Marth, G.T., McVean, G.A.: An integrated map of genetic variation from 1,092 human genomes. Nature 491(7422), 56–65 (2012)CrossRefGoogle Scholar
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    Kuleshov, V., Xie, D., Chen, R., Pushkarev, D., Ma, Z., Blauwkamp, T., Kertesz, M., Snyder, M.: Whole-genome haplotyping using long reads and statistical methods. Nat Biotechnol 32(3), 261–266 (2014)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Alex Bishara
    • 1
    Email author
  • Yuling Liu
    • 1
    • 2
  • Dorna Kashef-Haghighi
    • 1
  • Ziming Weng
    • 3
  • Daniel E. Newburger
    • 4
  • Robert West
    • 3
  • Arend Sidow
    • 3
    • 5
  • Serafim Batzoglou
    • 1
  1. 1.Department of Computer ScienceStanford UniversityStanfordUSA
  2. 2.Department of ChemistryStanford UniversityStanfordUSA
  3. 3.Department of PathologyStanford University School of MedicineStanfordUSA
  4. 4.Biomedical Informatics Training ProgramStanford UniversityStanfordUSA
  5. 5.Department of GeneticsStanford UniversityStanfordUSA

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