title: Disk-based compression of data from genome sequencing.
abstract: BACKGROUND
  High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, since the redundancy between overlapping reads cannot be easily captured in the (relatively small) main memory. More interesting solutions for this problem are disk based, where the better of these two, from Cox et al. (2012), is based on the Burrows-Wheeler transform (BWT) and achieves 0.518 bits per base for a 134.0 Gbp human genome sequencing collection with almost 45-fold coverage.
  
  
  RESULTS
  We propose overlapping reads compression with minimizers, a compression algorithm dedicated to sequencing reads (DNA only). Our method makes use of a conceptually simple and easily parallelizable idea of minimizers, to obtain 0.317 bits per base as the compression ratio, allowing to fit the 134.0 Gbp dataset into only 5.31 GB of space.
  
  
  METHODS
  http://sun.aei.polsl.pl/orcom under a free license.
  
  
  BACKGROUND
  sebastian.deorowicz@polsl.pl
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Institute of Applied Computer Science, Lodz University of Technology, Al. Politechniki 11, 90-924 Łódź, Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Polish-Japanese Institute of Information Technology, Koszykowa 86, 02-008 Warszawa, Poland and Centro Nacional de Análisis Genómico (CNAG), 08-028 Barcelona, Spain.
authors.forename: Szymon
authors.initials: S
authors.lastname: Grabowski
authors.affiliation: Institute of Applied Computer Science, Lodz University of Technology, Al. Politechniki 11, 90-924 Łódź, Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Polish-Japanese Institute of Information Technology, Koszykowa 86, 02-008 Warszawa, Poland and Centro Nacional de Análisis Genómico (CNAG), 08-028 Barcelona, Spain.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Deorowicz
authors.affiliation: Institute of Applied Computer Science, Lodz University of Technology, Al. Politechniki 11, 90-924 Łódź, Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Polish-Japanese Institute of Information Technology, Koszykowa 86, 02-008 Warszawa, Poland and Centro Nacional de Análisis Genómico (CNAG), 08-028 Barcelona, Spain Institute of Applied Computer Science, Lodz University of Technology, Al. Politechniki 11, 90-924 Łódź, Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Polish-Japanese Institute of Information Technology, Koszykowa 86, 02-008 Warszawa, Poland and Centro Nacional de Análisis Genómico (CNAG), 08-028 Barcelona, Spain.
authors.forename: Łukasz
authors.initials: Ł
authors.lastname: Roguski
mesh_terms: D000465:Algorithms; D000818:Animals; D002645:Chickens / Q000235:genetics; D044962:Data Compression; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*