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Pregled bibliografske jedinice broj: 915066

MinCall | MinION end2end convolutional deep learning basecaller


Miculinić, Neven; Ratković, Marko; Šikić, Mile
MinCall | MinION end2end convolutional deep learning basecaller // 2nd International workshop on deep learning for precision medicine, ECML-PKDD 2017
Skopje, Makedonija, 2017. str. 1-8 (predavanje, međunarodna recenzija, ostalo, znanstveni)


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Naslov
MinCall | MinION end2end convolutional deep learning basecaller

Autori
Miculinić, Neven ; Ratković, Marko ; Šikić, Mile

Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, ostalo, znanstveni

Izvornik
2nd International workshop on deep learning for precision medicine, ECML-PKDD 2017 / - , 2017, 1-8

Skup
2nd International workshop on deep learning for precision medicine, ECML-PKDD 2017

Mjesto i datum
Skopje, Makedonija, 18-22.9.2017

Vrsta sudjelovanja
Predavanje

Vrsta recenzije
Međunarodna recenzija

Ključne riječi
Basecaller, MinION, R9, CNN, CTC, Next generation sequencing

Sažetak
The Oxford Nanopore Technologies's MinION is the first portable DNA sequencing device. It is capable of producing long reads, over 100 kBp were reported. However, it has significantly higher error rate than other methods. In this study, we present MinCall, an end2end basecaller model for the MinION. The model is based on deep learning and uses convolutional neural networks (CNN) in its implementation. For extra performance, it uses cutting edge deep learning techniques and architectures, batch normalization and Connectionist Temporal Classification (CTC) loss. The best performing deep learning model achieves 91.4% median match rate on E. Coli dataset using R9 pore chemistry and 1D reads.

Izvorni jezik
Engleski

Znanstvena područja
Biologija, Računarstvo



POVEZANOST RADA


Ustanove
Fakultet elektrotehnike i računarstva, Zagreb

Profili:

Avatar Url Mile Šikić (autor)

Citiraj ovu publikaciju

Miculinić, Neven; Ratković, Marko; Šikić, Mile
MinCall | MinION end2end convolutional deep learning basecaller // 2nd International workshop on deep learning for precision medicine, ECML-PKDD 2017
Skopje, Makedonija, 2017. str. 1-8 (predavanje, međunarodna recenzija, ostalo, znanstveni)
Miculinić, N., Ratković, M. & Šikić, M. (2017) MinCall | MinION end2end convolutional deep learning basecaller. U: 2nd International workshop on deep learning for precision medicine, ECML-PKDD 2017.
@article{article, year = {2017}, pages = {1-8}, keywords = {Basecaller, MinION, R9, CNN, CTC, Next generation sequencing}, title = {MinCall | MinION end2end convolutional deep learning basecaller}, keyword = {Basecaller, MinION, R9, CNN, CTC, Next generation sequencing}, publisherplace = {Skopje, Makedonija} }