• Bedtk: finding interval overlap with implicit interval tree

    10 days ago - By Oxford Journals

    AbstractSummaryWe present bedtk, a new toolkit for manipulating genomic intervals in the BED format. It supports sorting, merging, intersection, subtraction and the calculation of the breadth of coverage. Bedtk uses implicit interval tree, a data structure for fast interval overlap queries. It is several to tens of times faster than existing tools and tends to use less memory.Availability and implementationThe source code is available at .
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