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Coding and processing of high-throughput sequencing data

TNT members involved in this project:
Dr.-Ing. Marco Munderloh
Prof. Dr.-Ing. Jörn Ostermann
Dipl.-Ing. Jan Voges

Over the past years, technological advances in sequencing (i.e., the process of reading out genomic information) have led to a faster and more cost-efficient approach to sequence individual genomes. Because of the enormous amount of sequencing data generated by high-throughput sequencing (HTS) machines, the processing, storage, and analysis of sequencing data entails novel challenges for the scientific community. Novel processes and tools have to be developed to overcome the current limitations in terms of storage space, processing speed, and many more.

Raw sequencing data generated by HTS machines passes through a great number of different analysis steps. Our goal is to develop novel algorithms to enhance the information processing "from the tissue to the hard drive".

Show recent publications only
  • Journals
    • 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, Nature Publishing Group, Vol. 13, No. 12, pp. 1005-1008, October 2016
  • Conference Contributions
    • 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), IEEE Computer Society Conference Publishing Services (CPS), pp. 444-444, April 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), IEEE Computer Society Conference Publishing Services (CPS), pp. 221-230, April 2016
    • Jan Voges, Marco Munderloh, Jörn Ostermann
      Predictive Coding of Aligned Next-Generation Sequencing Data
      2016 Data Compression Conference (DCC), IEEE Computer Society Conference Publishing Services (CPS), pp. 241-250, April 2016
  • Standardisation Contributions
    • Jan Voges, Mikel Hernaez
      Core Experiment 2 on Genomic Information Representation results LUH/Stanford/UIUC
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M40224, April 2017
    • Jan Voges, Claudio Alberti, Mikel Hernaez, Tom Paridaens, James Bonfield, Paolo Ribeca, Jaime Delgado
      Unified representation of sequencing quality values
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M40222, April 2017
    • Jan Voges
      Summary of Core Experiment 2 on Genomic Information Representation
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M40223, April 2017
    • Claudio Alberti, Jan Voges, Giorgio Zioa
      Unified representation of genomic reads
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M40277, April 2017
    • Jan Voges
      Core Experiment 2 summary
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M39663, Geneva (CH), January 2017
    • Jan Voges, Mikel Hernaez
      Core Experiment 2 results LUH-Stanford/UIUC
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M39664, Geneva (CH), January 2017
    • Jan Voges
      Core Experiment 1 results LUH
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M39665, Geneva (CH), January 2017
    • Jan Voges
      Core Experiment 3 results LUH
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M39666, Geneva (CH), January 2017
    • Jan Voges, Mikel Hernaez, Idoia Ochoa, Ana Angelica Hernandez-Lopez, Claudio Alberti, Marco Mattavelli, Al Wegener, Dan Greenfield, Noah Daniels, S Cenk Sahinalp, James Bonfield, Bonnie Berger, Jörn Ostermann
      Benchmark framework for lossy compression of genome sequencing quality values
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M38916, Chengdu (CN), October 2016
    • Jan Voges, Mikel Hernaez, Jörn Ostermann
      Adaptive lossy compression of high-throughput sequencing quality values
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M38917, Chengdu (CN), October 2016
    • Jan Voges, Marco Munderloh, Jörn Ostermann
      Reference-free compression of aligned high-throughput sequencing data
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M38918, Chengdu (CN), October 2016
    • Jan Voges, Mikel Hernaez, Ana Angelica Hernandez-Lopez, Claudio Alberti, Marco Mattavelli, Al Wegener, Dan Greenfield, Noah Daniels, S Cenk Sahinalp, James Bonfield, Bonnie Berger
      Extensions and notes to the evaluation framework for lossy compression of genome sequencing quality values
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M38376, Geneva (CH), May 2016
    • Jan Voges
      Reference-free Compression of Aligned Next-Generation Sequencing Data
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M37678, San Diego, CA (US), February 2016
    • Ibrahim Numanagic, Faraz Hach, James Bonfield, Claudio Alberti, Jan Voges
      Review of genomic information compression tools
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M37766, San Diego, CA (US), February 2016
    • Claudio Alberti, Marco Mattavelli, Ana A. Hernandez-Lopez, Mikel Hernaez, Rachel G. Goldfeder, Noah Daniels, Jan Voges
      Proposal for the update to the database of genomic test data
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M37767, San Diego, CA (US), February 2016
    • Claudio Alberti, Marco Mattavelli, Ana A. Hernandez-Lopez, Noah Daniels, Mikel Hernaez, Idoia Ochoa, Jan Voges, Rachel Goldfeder, Daniel Greenfield
      Evaluation framework for lossy compression of genomic Quality Values
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M37768, San Diego, CA (US), February 2016
    • Jan Voges
      A Framework for the Evaluation of Genomic Information Compression
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M37061, Geneva (CH), October 2015
    • Claudio Alberti, Marco Mattavelli, Ioannis Xenarios, Nicolas Guex, Heinz Stockinger, Thierry Schuepbach, Christian Iseli, Daniel Zerzion, Ivan Topolsky, Yann Thoma, Enrico Petraglio, Mikel Hernaez, Jan Voges
      A framework for the comparison of genomic information compression tools
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M37151, Geneva (CH), October 2015
    • Jan Voges, Marco Munderloh
      Approaches to SAM File Compression
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M36282, Warsaw (PL), June 2015