QVZ

QVZ is a lossy compression algorithm for quality values in genomic data files, such as FASTQ and SAM files. The proposed algorithm exhibits better rate-distortion performance than previously proposed algorithms, for several distortion metrics and for the lossless case. The user can define any quasi-convex distortion function to be minimized, a feature not supported by the previous algorithms. Additionally, QVZ-compressed data exhibit better performance in genotyping than data compressed with previously proposed algorithms.

Topic

DNA;Sequencing;Sequence analysis;Data quality management

Detail

  • Operation: Sequencing quality control

  • Software interface: Command-line user interface

  • Language: C

  • License: GNU General Public License v3.0

  • Cost: Free

  • Version name: -

  • Credit: Stanford Graduate Fellowships Program in Science and Engineering, the Basque Government, the Center for Science of Information (CSoI), NSF, NIH.

  • Input: -

  • Output: -

  • Contact: iochoa@stanford.edu;gmalysa@stanford.edu;mhernaez@stanford.edu

  • Collection: -

  • Maturity: -

Publications

Download and documentation

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