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Improving Genome Assemblies Using Multi-platform Sequence Data

  • Pınar KavakEmail author
  • Bekir Ergüner
  • Duran Üstek
  • Bayram Yüksel
  • Mahmut Şamil Sağıroğlu
  • Tunga Güngör
  • Can AlkanEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9874)

Abstract

Accurate de novo assembly using short reads generated by next generation sequencing technologies is still an open problem. Although there are several assembly algorithms developed for data generated with different sequencing technologies, and some that can make use of hybrid data, the assemblies are still far from being perfect. There is still a need for computational approaches to improve draft assemblies. Here we propose a new method to correct assembly mistakes when there are multiple types of data generated using different sequencing technologies that have different strengths and biases. We exploit the assembly of highly accurate short reads to correct the contigs obtained from less accurate long reads. We apply our method to Illumina, 454, and Ion Torrent data, and also compare our results with existing hybrid assemblers, Celera and Masurca.

Keywords

de novo assembly Assembly improvement Next generation multi-platform sequencing 

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Pınar Kavak
    • 1
    • 2
    Email author
  • Bekir Ergüner
    • 1
  • Duran Üstek
    • 3
  • Bayram Yüksel
    • 4
  • Mahmut Şamil Sağıroğlu
    • 1
  • Tunga Güngör
    • 2
  • Can Alkan
    • 5
    Email author
  1. 1.Advanced Genomics and Bioinformatics Research Group (İGBAM), BİLGEMThe Scientific and Technological Research Council of Turkey (TÜBİTAK)KocaeliTurkey
  2. 2.Department of Computer EngineeringBoğaziçi UniversityİstanbulTurkey
  3. 3.Department of Medical Geneticsİstanbul Medipol UniversityİstanbulTurkey
  4. 4.TÜBİTAK - MAM - GMBE (The Scientific and Technological Research Council of Turkey, Genetic Engineering and Biotechnology Institute)KocaeliTurkey
  5. 5.Department of Computer EngineeringBilkent UniversityAnkaraTurkey

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