Dataset Information
Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data.
Ontology highlight
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.
SUBMITTER: Harris RS
PROVIDER: S-EPMC6853708 | biostudies-literature | 2019 Nov
REPOSITORIES: biostudies-literature
Publications
Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data.
Bioinformatics (Oxford, England) 20191101 22
<h4>Summary</h4>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 v ...[more]