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Updated: Jan 22, 2026

DNA Fingerprinting of Mycobacterium leprae Strains Using Variable Number Tandem Repeat VNTR - Fragment Length Analysis FLA
Published on: July 15, 2011
Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data
Robert S Harris1, Monika Cechova1, Kateryna D Makova1,2
1Department of Biology, The Pennsylvania State University, State College, PA 16802, USA.
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, and is available in bioconda and at https://github.com/makovalab-psu/NoiseCancellingRepeatFinder.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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