Operating on Genomic Ranges Using BEDOPS

doi:10.1007/978-1-4939-3578-9_14

. 2016:1418:267-81.

doi: 10.1007/978-1-4939-3578-9_14.

Operating on Genomic Ranges Using BEDOPS

Shane Neph¹, Alex P Reynolds¹, M Scott Kuehn², John A Stamatoyannopoulos^{3

4

5}

Affiliations

¹ Department of Genome Sciences, Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, Seattle, WA, 98195, USA.
² Opower Inc., 760 Market Street, San Francisco, CA, 94102, USA.
³ Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, Seattle, WA, 98195, USA. jstam@uw.edu.
⁴ Department of Medicine, University of Washington, Seattle, WA, USA. jstam@uw.edu.
⁵ Department of Genome Sciences, University of Washington, Seattle, WA, USA. jstam@uw.edu.

PMID: 27008020
DOI: 10.1007/978-1-4939-3578-9_14

Operating on Genomic Ranges Using BEDOPS

Shane Neph et al. Methods Mol Biol. 2016.

. 2016:1418:267-81.

doi: 10.1007/978-1-4939-3578-9_14.

Authors

Shane Neph¹, Alex P Reynolds¹, M Scott Kuehn², John A Stamatoyannopoulos^{3

4

5}

Affiliations

¹ Department of Genome Sciences, Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, Seattle, WA, 98195, USA.
² Opower Inc., 760 Market Street, San Francisco, CA, 94102, USA.
³ Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, Seattle, WA, 98195, USA. jstam@uw.edu.
⁴ Department of Medicine, University of Washington, Seattle, WA, USA. jstam@uw.edu.
⁵ Department of Genome Sciences, University of Washington, Seattle, WA, USA. jstam@uw.edu.

PMID: 27008020
DOI: 10.1007/978-1-4939-3578-9_14

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.

Keywords: Algorithm; Bioinformatics; Compression; Genomics; Overlap; Parallelization; Sequencing.

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Operating on Genomic Ranges Using BEDOPS

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Operating on Genomic Ranges Using BEDOPS

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