Noise-cancelling Repeat Finder: Uncovering Tandem Repeats in Error-prone Long-read Sequencing Data

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2019 Jul 11

PMID 31290946

Citations 29

Authors

Robert S Harris

Monika Cechova

Kateryna D Makova

Affiliations

Soon will be listed here.

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, 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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