Datenbank-Spektrum

, Volume 15, Issue 3, pp 185–191 | Cite as

Genome sequence analysis with MonetDB

A case study on Ebola virus diversity
  • Robin Cijvat
  • Stefan Manegold
  • Martin Kersten
  • Gunnar W. Klau
  • Alexander Schönhuth
  • Tobias Marschall
  • Ying Zhang
SCHWERPUNKTBEITRAG

Abstract

Next-generation sequencing (NGS) technology has led the life sciences into the big data era. Today, sequencing genomes takes little time and cost, but yields terabytes of data to be stored and analyzed. Biologists are often exposed to excessively time consuming and error-prone data management and analysis hurdles. In this paper, we propose a database management system (DBMS) based approach to accelerate and substantially simplify genome sequence analysis. We have extended MonetDB, an open-source column-based DBMS, with a BAM module, which enables easy, flexible, and rapid management and analysis of sequence alignment data stored as Sequence Alignment/Map (SAM/BAM) files. We describe the main features of MonetDB/BAM using a case study on Ebola virus

genomes.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Robin Cijvat
    • 1
  • Stefan Manegold
    • 2
  • Martin Kersten
    • 1
    • 2
  • Gunnar W. Klau
    • 2
  • Alexander Schönhuth
    • 2
  • Tobias Marschall
    • 3
  • Ying Zhang
    • 1
    • 2
  1. 1.MonetDB SolutionsAmsterdamThe Netherlands
  2. 2.Centrum Wiskunde & InformaticaAmsterdamThe Netherlands
  3. 3.Saarland University & Max Planck Institute for InformaticsSaarbrückenGermany

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