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PyRanges: efficient comparison of genomic intervals in Python

By Endre Bakken Stovner, Pål Sætrom

Posted 16 Apr 2019
bioRxiv DOI: 10.1101/609396 (published DOI: 10.1093/bioinformatics/btz615)

Summary: Complex genomic analyses often use sequences of simple set operations like intersection, overlap, and nearest on genomic intervals. These operations, coupled with some custom programming, allow a wide range of analyses to be performed. To this end, we have written PyRanges, a data structure for representing and manipulating genomic intervals and their associated data in Python. Run single-threaded on binary set operations, PyRanges is in median 2.3-9.6 times faster than the popular R GenomicRanges library and is equally memory efficient; run multi-threaded on 8 cores, our library is up to 123 times faster. PyRanges is therefore ideally suited both for individual analyses and as a foundation for future genomic libraries in Python. Availability: PyRanges is available open-source under the MIT license at https://github.com/biocore-NTNU/pyranges and documentation exists at https://biocore-NTNU.github.io/pyranges/ Contact: endrebak85@gmail.com Supplementary information: Supplementary data are available.

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