Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

Haotian Teng, Minh Duc Cao, Michael B Hall, Tania Duarte, Sheng Wang, Lachlan J M Coin

Research output: Contribution to journalArticlepeer-review

53 Scopus citations

Abstract

Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology that offers faster and cheaper sequencing than other approaches. However, accurately deciphering the DNA sequence from the noisy and complex electrical signal is challenging. Here, we report Chiron, the first deep learning model to achieve end-to-end basecalling and directly translate the raw signal to DNA sequence without the error-prone segmentation step. Trained with only a small set of 4,000 reads, we show that our model provides state-of-the-art basecalling accuracy, even on previously unseen species. Chiron achieves basecalling speeds of more than 2,000 bases per second using desktop computer graphics processing units.
Original languageEnglish (US)
JournalGigaScience
Volume7
Issue number5
DOIs
StatePublished - Apr 10 2018

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