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An End-to-end Oxford Nanopore Basecaller Using Convolution-augmented Transformer

View ORCID ProfileXuan Lv, Zhiguang Chen, Yutong Lu, View ORCID ProfileYuedong Yang
doi: https://doi.org/10.1101/2020.11.09.374165
Xuan Lv
1School of Computer Science, National University of Defense Technology, Changsha, China
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Zhiguang Chen
2School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China
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Yutong Lu
2School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China
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Yuedong Yang
2School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China
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  • For correspondence: yangyd25@mail.sysu.edu.cn
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Abstract

Oxford Nanopore sequencing is fastly becoming an active field in genomics, and it’s critical to basecall nucleotide sequences from the complex electrical signals. Many efforts have been devoted to developing new basecalling tools over the years. However, the basecalled reads still suffer from a high error rate and slow speed. Here, we developed an open-source basecalling method, CATCaller, by simultaneously capturing global context through Attention and modeling local dependencies through dynamic convolution. The method was shown to consistently outper-form the ONT default basecaller Albacore, Guppy, and a recently developed attention-based method SACall in read accuracy. More importantly, our method is fast through a heterogeneously computational model to integrate both CPUs and GPUs. When compared to SACall, the method is nearly 4 times faster on a single GPU, and is highly scalable in parallelization with a further speedup of 3.3 on a four-GPU node.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • lvxuan14{at}nudt.edu.cn, zhiguang.chen{at}nscc-gz.cn, yutong.lu{at}nscc-gz.cn, yangyd25{at}mail.sysu.edu.cn

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted November 10, 2020.
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An End-to-end Oxford Nanopore Basecaller Using Convolution-augmented Transformer
Xuan Lv, Zhiguang Chen, Yutong Lu, Yuedong Yang
bioRxiv 2020.11.09.374165; doi: https://doi.org/10.1101/2020.11.09.374165
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An End-to-end Oxford Nanopore Basecaller Using Convolution-augmented Transformer
Xuan Lv, Zhiguang Chen, Yutong Lu, Yuedong Yang
bioRxiv 2020.11.09.374165; doi: https://doi.org/10.1101/2020.11.09.374165

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