Compression of DNA Sequencing Data

TNT members involved in this project:
Yeremia G. Adhisantoso, M.Sc.
Dr.-Ing. Marco Munderloh
Prof. Dr.-Ing. Jörn Ostermann
Dipl.-Ing. Jan Voges

Over the past years technological advances in DNA sequencing have led to faster and more cost-efficient approaches to sequence individual genomes and other genomic samples. Because of the enormous amount of sequencing data generated the processing, storage and analysis of sequencing data entails novel challenges for the scientific community. New processes and tools have to be developed to overcome the current limitations in terms of storage space, processing speed and many more. Our goal is to develop novel algorithms to enhance data processing "from the tissue to the hard drive".

In the scope of this project we actively contribute to the series of MPEG-G standards (ISO/IEC 23092). More information is available on the MPEG-G website.

Show recent publications only
  • Conference Contributions
    • Idoia Ochoa, Hongyi Li, Florian Baumgarte, Charles Hergenrother, Jan Voges, Mikel Hernaez
      AliCo: A New Efficient Representation for SAM Files
      2019 Data Compression Conference (DCC), pp. 93-102, 2019
    • Tom Paridaens, Jan Voges, Mikel Hernaez, Jan Fostier, Jörn Ostermann
      GABAC: an arithmetic coding solution for genomic data [version 1; not peer-reviewed]
      F1000Research (International Society for Computational Biology Community Journal), Vol. 8, p. 1463 (poster), 2019
    • Jan Voges, Ali Fotouhi, Jörn Ostermann, M. Oguzhan Külekci
      A Two-Level Scheme for Quality Score Compression
      10th International Conference on Bioinformatics and Computational Biology (BICOB 2018), pp. 93-102, 2018
    • Ana A. Hernandez-Lopez, Jan Voges, Claudio Alberti, Marco Mattavelli, Jörn Ostermann
      Lossy Compression of Quality Scores in Differential Gene Expression: A First Assessment and Impact Analysis
      2018 Data Compression Conference (DCC), pp. 167-176, 2018
    • Ana A. Hernandez-Lopez, Jan Voges, Claudio Alberti, Marco Mattavelli, Jörn Ostermann
      Differential Gene Expression with Lossy Compression of Quality Scores in RNA-Seq Data
      2017 Data Compression Conference (DCC), p. 444 (poster), 2017
    • Jan Voges, Jörn Ostermann, Mikel Hernaez
      CALQ: compression of quality values of aligned sequencing data [version 1; not peer-reviewed]
      F1000Research (International Society for Computational Biology Community Journal), Vol. 6, p. 1382 (poster), 2017
    • Jan Voges, Jörn Ostermann
      MPEG-G: The Emerging Standard for Genomic Data [not peer-reviewed]
      Poster abstracts of the 25th German Conference on Bioinformatics, p. 2 (poster), 2017
    • Claudio Alberti, Noah Daniels, Mikel Hernaez, Jan Voges, Rachel L. Goldfeder, Ana A. Hernandez-Lopez, Marco Mattavelli, Bonnie Berger
      An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values
      2016 Data Compression Conference (DCC), pp. 221-230, 2016
    • Jan Voges, Marco Munderloh, Jörn Ostermann
      Predictive Coding of Aligned Next-Generation Sequencing Data
      2016 Data Compression Conference (DCC), pp. 241-250, 2016
  • Journals
    • Jan Voges, Mikel Hernaez, Marco Mattavelli, Jörn Ostermann
      An Introduction to MPEG-G: The First Open ISO/IEC Standard for the Compression and Exchange of Genomic Sequencing Data
      Proceedings of the IEEE, Vol. 109, No. 9, pp. 1607-1622, 2021
    • Jan Voges, Tom Paridaens, Fabian Müntefering, Liudmila S. Mainzer, Brian Bliss, Mingyu Yang, Idoia Ochoa, Jan Fostier, Jörn Ostermann, Mikel Hernaez
      GABAC: an arithmetic coding solution for genomic data
      Bioinformatics, Vol. 36, No. 7, pp. 2275-2277, 2020
    • Jan Voges, Jörn Ostermann, Mikel Hernaez
      CALQ: compression of quality values of aligned sequencing data
      Bioinformatics, Vol. 34, No. 10, pp. 1650-1658, 2018
    • Jan Voges, Ali Fotouhi, Jörn Ostermann, M. Oguzhan Külekci
      A Two-level Scheme for Quality Score Compression
      Journal of Computational Biology, Vol. 25, No. 10, pp. 1141-1151, 2018
    • Claudio Alberti, Tom Paridaens, Jan Voges, Daniel Naro, Junaid J. Ahmad, Massimo Ravasi, Daniele Renzi, Giorgio Zoia, Paolo Ribeca, Idoia Ochoa, Marco Mattavelli, Jaime Delgado, Mikel Hernaez
      An introduction to MPEG-G, the new ISO standard for genomic information representation [not peer-reviewed]
      bioRxiv, Vol. 426353, 2018
    • Ibrahim Numanagic, James K. Bonfield, Faraz Hach, Jan Voges, Jörn Ostermann, Claudio Alberti, Marco Mattavelli, S. Cenk Sahinalp
      Comparison of high-throughput sequencing data compression tools
      Nature Methods, Vol. 13, No. 12, pp. 1005-1008, 2016
  • Technical Report
    • Jörn Ostermann, Jan Voges
      Streaming für die Genomforschung [not peer-reviewed]
      Binaire, Vol. 2019, No. 2, 2019