title: BEDOPS: high-performance genomic feature operations.
abstract: The large and growing number of genome-wide datasets highlights the need for high-performance feature analysis and data comparison methods, in addition to efficient data storage and retrieval techniques. We introduce BEDOPS, a software suite for common genomic analysis tasks which offers improved flexibility, scalability and execution time characteristics over previously published packages. The suite includes a utility to compress large inputs into a lossless format that can provide greater space savings and faster data extractions than alternatives.
  
  
  BACKGROUND
  http://code.google.com/p/bedops/ includes binaries, source and documentation.
authors.affiliation: Department of Genome Sciences and Department of Medicine, University of Washington, Seattle, Washington, DC 98195, USA. sjn@u.washington.edu
authors.forename: Shane
authors.initials: S
authors.lastname: Neph
authors.forename: M Scott
authors.initials: MS
authors.lastname: Kuehn
authors.forename: Alex P
authors.initials: AP
authors.lastname: Reynolds
authors.forename: Eric
authors.initials: E
authors.lastname: Haugen
authors.forename: Robert E
authors.initials: RE
authors.lastname: Thurman
authors.forename: Audra K
authors.initials: AK
authors.lastname: Johnson
authors.forename: Eric
authors.initials: E
authors.lastname: Rynes
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Maurano
authors.forename: Jeff
authors.initials: J
authors.lastname: Vierstra
authors.forename: Sean
authors.initials: S
authors.lastname: Thomas
authors.forename: Richard
authors.initials: R
authors.lastname: Sandstrom
authors.forename: Richard
authors.initials: R
authors.lastname: Humbert
authors.forename: John A
authors.initials: JA
authors.lastname: Stamatoyannopoulos
mesh_terms: D044962:Data Compression / Q000379:methods*; D023281:Genomics / Q000379:methods*; D012984:Software