Detail publikace

Reference-free Identification of Phage DNA Using Signal Processing on Nanopore Data

Originální název

Reference-free Identification of Phage DNA Using Signal Processing on Nanopore Data

Anglický název

Reference-free Identification of Phage DNA Using Signal Processing on Nanopore Data

Jazyk

en

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.

Anglický 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.

BibTex


@inproceedings{BUT140931,
  author="Kristýna {Kupková} and Karel {Sedlář} and Ivo {Provazník}",
  title="Reference-free Identification of Phage DNA Using Signal Processing on Nanopore
Data",
  annote="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.",
  address="Conference Publishing Services",
  booktitle="2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017",
  chapter="140931",
  doi="10.1109/BIBE.2017.00-71",
  howpublished="online",
  institution="Conference Publishing Services",
  year="2017",
  month="october",
  pages="101--105",
  publisher="Conference Publishing Services",
  type="conference paper"
}