title: Operating on Genomic Ranges Using BEDOPS.
abstract: The bulk of modern genomics research includes, in part, analyses of large data sets, such as those derived from high resolution, high-throughput experiments, that make computations challenging. The BEDOPS toolkit offers a broad spectrum of fundamental analysis capabilities to query, operate on, and compare quantitatively genomic data sets of any size and number. The toolkit facilitates the construction of complex analysis pipelines that remain efficient in both memory and time by chaining together combinations of its complementary components. The principal utilities accept raw or compressed data in a flexible format, and they provide built-in features to expedite parallel computations.
authors.affiliation: Department of Genome Sciences, Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, Seattle, WA, 98195, USA.
authors.forename: Shane
authors.initials: S
authors.lastname: Neph
authors.affiliation: Department of Genome Sciences, Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, Seattle, WA, 98195, USA.
authors.forename: Alex P
authors.initials: AP
authors.lastname: Reynolds
authors.affiliation: Opower Inc., 760 Market Street, San Francisco, CA, 94102, USA.
authors.forename: M Scott
authors.initials: MS
authors.lastname: Kuehn
authors.affiliation: Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, Seattle, WA, 98195, USA. jstam@uw.edu.|Department of Medicine, University of Washington, Seattle, WA, USA. jstam@uw.edu.|Department of Genome Sciences, University of Washington, Seattle, WA, USA. jstam@uw.edu.
authors.forename: John A
authors.initials: JA
authors.lastname: Stamatoyannopoulos
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D044962:Data Compression; D016678:Genome; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D017421:Sequence Analysis / Q000379:methods; D012984:Software
keywords: Algorithm; Bioinformatics; Compression; Genomics; Overlap; Parallelization; Sequencing