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KUPKOVÁ, K. SEDLÁŘ, K. PROVAZNÍK, I.
Originální název
Reference-free Identification of Phage DNA Using Signal Processing on Nanopore Data
Typ
článek ve sborníku ve WoS nebo Scopus
Jazyk
angličtina
Originální abstrakt
Nanopore sequencing has become an invaluable aid in small sequencing projects. Thanks to its compact size, the Oxford Nanopore MinION platform is often used in crisis situations, such as outbreaks of microbial infections, to determine the causes of the problem. As a platform that produces data in real-time, it requires bioinformatics techniques designed for fast data processing. In this paper, we demonstrate the possibility of the direct processing of nanopore current signals, the so-called squiggles, for fast reference-free identification of phage DNA. The proposed technique is based on the computation of Hjorth parameters and is suitable for fast visualization of the data, as well as for proper classification by many machine learning algorithms. The classification of the data also raises the possibility of applying adapted base calling algorithms for both groups separately, as phage and host DNA have different features.
Klíčová slova
nanopore sequencing; shotgun; signal processing; phage; SVM; AdaBoost; random forrest
Autoři
KUPKOVÁ, K.; SEDLÁŘ, K.; PROVAZNÍK, I.
Vydáno
23. 10. 2017
Nakladatel
Conference Publishing Services
Místo
Washington DC
ISBN
978-1-5386-1324-5
Kniha
2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017
Strany od
101
Strany do
105
Strany počet
584
BibTex
@inproceedings{BUT140931, author="Kristýna {Kupková} and Karel {Sedlář} and Valentine {Provazník}", title="Reference-free Identification of Phage DNA Using Signal Processing on Nanopore Data", booktitle="2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017", year="2017", pages="101--105", publisher="Conference Publishing Services", address="Washington DC", doi="10.1109/BIBE.2017.00-71", isbn="978-1-5386-1324-5" }