DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing.
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ABSTRACT:
SUBMITTER: Fang L
PROVIDER: S-EPMC9052667 | biostudies-literature | 2022 Apr
REPOSITORIES: biostudies-literature
Publications
DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing.
Fang Li L Liu Qian Q Monteys Alex Mas AM Gonzalez-Alegre Pedro P Davidson Beverly L BL Wang Kai K
Genome biology 20220428 1
Despite recent improvements in basecalling accuracy, nanopore sequencing still has higher error rates on short-tandem repeats (STRs). Instead of using basecalled reads, we developed DeepRepeat which converts ionic current signals into red-green-blue channels, thus transforming the repeat detection problem into an image recognition problem. DeepRepeat identifies and accurately quantifies telomeric repeats in the CHM13 cell line and achieves higher accuracy in quantifying repeats in long STRs than ...[more]
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