Operating on Genomic Ranges Using BEDOPS.

Neph S1, Reynolds AP1, Kuehn MS2, Stamatoyannopoulos JA3,4,5.

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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.