Finding long tandem repeats in long noisy reads.

Morishita, Shinichi; Ichikawa, Kazuki; Myers, Eugene W

doi:10.1093/bioinformatics/btaa865

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Finding long tandem repeats in long noisy reads.

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Myers, Eugene W
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

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Citation

Morishita, S., Ichikawa, K., & Myers, E. W. (2021). Finding long tandem repeats in long noisy reads. Bioinformatics (Oxford, England), 37(5), 612-621. doi:10.1093/bioinformatics/btaa865.

Cite as: https://hdl.handle.net/21.11116/0000-0008-DAA8-5

Abstract

Long tandem repeat expansions of more than 1000 nt have been suggested to be associated with diseases, but remain largely unexplored in individual human genomes because read lengths have been too short. However, new long-read sequencing technologies can produce single reads of 10 000 nt or more that can span such repeat expansions, although these long reads have high error rates, of 10-20%, which complicates the detection of repetitive elements. Moreover, most traditional algorithms for finding tandem repeats are designed to find short tandem repeats (<1000 nt) and cannot effectively handle the high error rate of long reads in a reasonable amount of time.