Compression of DNA sequence reads in FASTQ format

Bioinformatics. 2011 Mar 15;27(6):860-2. doi: 10.1093/bioinformatics/btr014. Epub 2011 Jan 19.

Abstract

Motivation: Modern sequencing instruments are able to generate at least hundreds of millions short reads of genomic data. Those huge volumes of data require effective means to store them, provide quick access to any record and enable fast decompression.

Results: We present a specialized compression algorithm for genomic data in FASTQ format which dominates its competitor, G-SQZ, as is shown on a number of datasets from the 1000 Genomes Project (www.1000genomes.org).

Availability: DSRC is freely available at http:/sun.aei.polsl.pl/dsrc.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Base Sequence
  • Computational Biology / methods
  • Data Compression / methods*
  • Genomics
  • Internet
  • Sequence Analysis, DNA*