Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network

Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network

Abstract Background Basecalling long DNA sequences is a crucial step in nanopore-based DNA sequencing protocols. In recent years, the CTC-RNN model has become the leading basecalling model, supplanting preceding hidden Markov models (HMMs) that relied on pre-segmenting ion current measurements. Howe...

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Bibliographic Details
Main Authors: Xuechun Xu, Nayanika Bhalla, Patrik Ståhl, Joakim Jaldén
Format: Article
Language:English
Published: BMC 2023-12-01
Series:BMC Bioinformatics
Subjects:
Basecalling
HMM
LSTM
Nanopore sequencing
Online Access:https://doi.org/10.1186/s12859-023-05580-x

Internet

https://doi.org/10.1186/s12859-023-05580-x

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