Bedtk: finding interval overlap with implicit interval tree.
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- Record sourced from PubMed, PMID 32966548.
- Also identified by DOI 10.1093/bioinformatics/btaa827 and PMC identifier 8189672.
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Abstract
We 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. The source code is available at https://github.com/lh3/bedtk.
Medical subject headings
- Software
- Trees