title: Comparison of high-throughput sequencing data compression tools.
abstract: High-throughput sequencing (HTS) data are commonly stored as raw sequencing reads in FASTQ format or as reads mapped to a reference, in SAM format, both with large memory footprints. Worldwide growth of HTS data has prompted the development of compression methods that aim to significantly reduce HTS data size. Here we report on a benchmarking study of available compression methods on a comprehensive set of HTS data using an automated framework.
authors: School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada.
authors: Ibrahim
authors: I
authors: Numanagić
authors: Wellcome Trust Sanger Institute, Hinxton, UK.
authors: James K
authors: JK
authors: Bonfield
authors: School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada.|Vancouver Prostate Centre, Vancouver, British Columbia, Canada.
authors: Faraz
authors: http://orcid.org/0000-0003-1143-0172
authors: F
authors: Hach
authors: Institut für Informationsverarbeitung, Leibniz Universität, Hannover, Germany.
authors: Jan
authors: J
authors: Voges
authors: Institut für Informationsverarbeitung, Leibniz Universität, Hannover, Germany.
authors: Jörn
authors: J
authors: Ostermann
authors: École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
authors: Claudio
authors: C
authors: Alberti
authors: École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
authors: Marco
authors: M
authors: Mattavelli
authors: School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada.|Vancouver Prostate Centre, Vancouver, British Columbia, Canada.|School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA.
authors: S Cenk
authors: SC
authors: Sahinalp
mesh_terms: D000818:Animals; D002099:Cacao / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D044962:Data Compression / Q000379:methods*; D004331:Drosophila melanogaster / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D011550:Pseudomonas aeruginosa / Q000235:genetics