Bedtk: finding interval overlap with implicit interval tree | Zendy

Heng Li | Zendy; Jiazhen Rong | Zendy

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Bedtk: finding interval overlap with implicit interval tree

Author(s) -

Heng Li,

Jiazhen Rong

Publication year - 2020

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btaa827

Subject(s) - interval (graph theory) , computer science , sorting , subtraction , intersection (aeronautics) , tree (set theory) , code (set theory) , interval tree , algorithm , theoretical computer science , tree structure , data structure , programming language , binary tree , arithmetic , mathematics , set (abstract data type) , combinatorics , engineering , aerospace engineering

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.

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