DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing.
Genome Biol
; 23(1): 108, 2022 04 28.
Article
em En
| MEDLINE
| ID: mdl-35484600
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 competing methods. We also evaluate DeepRepeat on genome-wide or candidate region datasets from seven different sources. In summary, DeepRepeat enables accurate quantification of long STRs and complements existing methods relying on basecalled reads.
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MEDLINE
Assunto principal:
Nanoporos
/
Sequenciamento por Nanoporos
Idioma:
En
Ano de publicação:
2022
Tipo de documento:
Article