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Bedtk: Finding Interval Overlap with Implicit Interval Tree [article]

Heng Li, Jiazhen Rong
2020 bioRxiv   pre-print
Bedtk employs implicit interval tree, a new data structure for fast interval overlap queries. It is several to tens of times faster than existing tools and tends to use less memory.  ...  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.  ...  Jones and Mike Lin for further improving the performance of implicit interval trees. Funding This work has been supported by NIH grant R01HG010040. Conflict of Interest: None declared.  ... 
doi:10.1101/2020.07.07.190744 fatcat:iknnkakve5bcxlniddffs2gd3a