Bedtk: finding interval overlap with implicit interval tree

Heng Li; Jiazhen Rong

doi:10.1093/bioinformatics/btaa827

Bedtk: finding interval overlap with implicit interval tree

Bioinformatics. 2021 Jun 9;37(9):1315-1316. doi: 10.1093/bioinformatics/btaa827.

Authors

Heng Li^{1

2}, Jiazhen Rong²

Affiliations

¹ Department of Data Science, Dana-Faber Cancer Institute, Boston, MA 02215, USA.
² Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02215, USA.

Abstract

Summary: 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.

Availability and implementation: The source code is available at https://github.com/lh3/bedtk.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Genome
Genomics
Software*
Trees*

Grants and funding

R01 HG010040/HG/NHGRI NIH HHS/United States