DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing

DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing

Abstract 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 de...

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Bibliographic Details
Main Authors: Li Fang, Qian Liu, Alex Mas Monteys, Pedro Gonzalez-Alegre, Beverly L. Davidson, Kai Wang
Format: Article
Language:English
Published: BMC 2022-04-01
Series:Genome Biology
Subjects:
Short tandem repeat
Nanopore sequencing
Deep learning
Telomeric repeat
Online Access:https://doi.org/10.1186/s13059-022-02670-6

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