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Compressing Resequencing Data with GReEn

  • Armando J. Pinho
  • Diogo Pratas
  • Sara P. Garcia
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1038)

Abstract

Genome sequencing centers are flooding the scientific community with data. A single sequencing machine can nowadays generate more data in one day than any existing machine could have produced throughout the entire year of 2005. Therefore, the pressure for efficient sequencing data compression algorithms is very high and is being felt worldwide. Here, we describe GReEn (Genome Resequencing Encoding), a compression tool recently proposed for compressing genome resequencing data using a reference genome sequence.

Key words

Data compression DNA sequences Probabilistic models Arithmetic coding Open source software 

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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Armando J. Pinho
    • 1
  • Diogo Pratas
    • 1
  • Sara P. Garcia
    • 1
  1. 1.IEETA/DETI, University of AveiroAveiroPortugal

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