Design of an Efficient Out-of-Core Read Alignment Algorithm

  • Arun S. Konagurthu
  • Lloyd Allison
  • Thomas Conway
  • Bryan Beresford-Smith
  • Justin Zobel
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6293)


New genome sequencing technologies are poised to enter the sequencing landscape with significantly higher throughput of read data produced at unprecedented speeds and lower costs per run. However, current in-memory methods to align a set of reads to one or more reference genomes are ill-equipped to handle the expected growth of read-throughput from newer technologies.

This paper reports the design of a new out-of-core read mapping algorithm, Syzygy, which can scale to large volumes of read and genome data. The algorithm is designed to run in a constant, user-stipulated amount of main memory – small enough to fit on standard desktops – irrespective of the sizes of read and genome data. Syzygy achieves a superior spatial locality-of-reference that allows all large data structures used in the algorithm to be maintained on disk. We compare our prototype implementation with several popular read alignment programs. Our results demonstrate clearly that Syzygy can scale to very large read volumes while using only a fraction of memory in comparison, without sacrificing performance.


Main Memory Reverse Complement Tile Size Radix Sort Genome Sequencing Technology 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Arun S. Konagurthu
    • 1
    • 2
  • Lloyd Allison
    • 1
  • Thomas Conway
    • 1
    • 2
  • Bryan Beresford-Smith
    • 1
    • 2
  • Justin Zobel
    • 2
    • 1
  1. 1.National ICT Australia (NICTA) Victoria Research Laboratory, Department of Electronics and Electrical EngineeringThe University of MelbourneParkvilleAustralia
  2. 2.Department of Computer Science and Software EngineeringThe University of MelbourneParkvilleAustralia

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