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Datenbank-Spektrum

, Volume 17, Issue 2, pp 139–154 | Cite as

Efficiently Storing and Analyzing Genome Data in Database Systems

  • Sebastian DorokEmail author
  • Sebastian Breß
  • Jens Teubner
  • Horstfried Läpple
  • Gunter Saake
  • Volker Markl
Fachbeitrag

Abstract

Genome-analysis enables researchers to detect mutations within genomes and deduce their consequences. Researchers need reliable analysis platforms to ensure reproducible and comprehensive analysis results. Database systems provide vital support to implement the required sustainable procedures. Nevertheless, they are not used throughout the complete genome-analysis process, because (1) database systems suffer from high storage overhead for genome data and (2) they introduce overhead during domain-specific analysis. To overcome these limitations, we integrate genome-specific compression into database systems using a specialized database schema. Thus, we can reduce the storage consumption of a database approach by up to 35%. Moreover, we exploit genome-data characteristics during query processing allowing us to analyze real-world data sets up to five times faster than specialized analysis tools and eight times faster than a straightforward database approach.

Keywords

Main-memory database systems Genome analysis Variant calling 

Notes

Acknowledgements

The work has received funding from the German Research Foundation (DFG), Collaborative Research Center SFB 876, project C5, from the European Union’s Horizon2020 Research & Innovation Program under grant agreement 671500 (project SAGE), and by the German Ministry for Education and Research as Berlin Big Data Center BBDC (01IS14013A).

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Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Sebastian Dorok
    • 1
    Email author
  • Sebastian Breß
    • 2
    • 3
  • Jens Teubner
    • 4
  • Horstfried Läpple
    • 5
  • Gunter Saake
    • 1
  • Volker Markl
    • 2
    • 3
  1. 1.University MagdeburgMagdeburgGermany
  2. 2.DFKI GmbHBerlinGermany
  3. 3.TU BerlinBerlinGermany
  4. 4.TU DortmundDortmundGermany
  5. 5.Bayer HealthCare AGBerlinGermany

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