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BEDOPS: high-performance genomic feature operations.

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. AVAILABILITY: includes binaries, source and documentation.

Pubmed ID: 22576172


  • Neph S
  • Kuehn MS
  • Reynolds AP
  • Haugen E
  • Thurman RE
  • Johnson AK
  • Rynes E
  • Maurano MT
  • Vierstra J
  • Thomas S
  • Sandstrom R
  • Humbert R
  • Stamatoyannopoulos JA


Bioinformatics (Oxford, England)

Publication Data

July 15, 2012

Associated Grants

  • Agency: NHGRI NIH HHS, Id: 1U54HG004592
  • Agency: NIEHS NIH HHS, Id: 5U01ES017156

Mesh Terms

  • Data Compression
  • Genomics
  • Software