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Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data

Robert S. Harris, Monika Cechova, Kateryna D. Makova
doi: https://doi.org/10.1101/475194
Robert S. Harris
1Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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Monika Cechova
1Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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Kateryna D. Makova
1Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
2Center for Medical Genomics, The Pennsylvania State University, University Park, PA 16802, USA
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ABSTRACT

Summary Tandem DNA repeats can be sequenced with long-read technologies, but cannot be accurately deciphered due to the lack of computational tools taking high error rates of these technologies into account. Here we introduce Noise-Cancelling Repeat Finder (NCRF) to uncover putative tandem repeats of specified motifs in noisy long reads produced by Pacific Biosciences and Oxford Nanopore sequencers. Using simulations, we validated the use of NCRF to locate tandem repeats with motifs of various lengths and demonstrated its superior performance as compared to two alternative tools. Using real human whole-genome sequencing data, NCRF identified long arrays of the (AATGG)n repeat involved in heat shock stress response.

Availability and implementation NCRF is implemented in C, supported by several python scripts. Source code, under the MIT open source license, and simulation data are available at https://github.com/makovalab-psu/NoiseCancellingRepeatFinder, and also in bioconda.

Footnotes

  • Contact rsharris{at}bx.psu.edu

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 22, 2018.
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Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data
Robert S. Harris, Monika Cechova, Kateryna D. Makova
bioRxiv 475194; doi: https://doi.org/10.1101/475194
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Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data
Robert S. Harris, Monika Cechova, Kateryna D. Makova
bioRxiv 475194; doi: https://doi.org/10.1101/475194

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