Detail publikačního výsledku

CNproScan: Hybrid CNV detection for bacterial genomes

JUGAS, R.; SEDLÁŘ, K.; VÍTEK, M.; NYKRÝNOVÁ, M.; BARTOŇ, V.; BEZDÍČEK, M.; LENGEROVÁ, M.; ŠKUTKOVÁ, H.

Originální název

CNproScan: Hybrid CNV detection for bacterial genomes

Anglický název

CNproScan: Hybrid CNV detection for bacterial genomes

Druh

Článek WoS

Originální abstrakt

Discovering copy number variation (CNV) in bacteria is not in the spotlight compared to the attention focused on CNV detection in eukaryotes. However, challenges arising from bacterial drug resistance bring further interest to the topic of CNV and its role in drug resistance. General CNV detection methods do not consider bacteria's features and there is space to improve detection accuracy. Here, we present a CNV detection method called CNproScan focused on bacterial genomes. CNproScan implements a hybrid approach and other bacteria-focused features and depends only on NGS data. We benchmarked our method and compared it to the previously published methods and we can resolve to achieve a higher detection rate together with providing other beneficial features, such as CNV classification. Compared with other methods, CNproScan can detect much shorter CNV events.

Anglický abstrakt

Discovering copy number variation (CNV) in bacteria is not in the spotlight compared to the attention focused on CNV detection in eukaryotes. However, challenges arising from bacterial drug resistance bring further interest to the topic of CNV and its role in drug resistance. General CNV detection methods do not consider bacteria's features and there is space to improve detection accuracy. Here, we present a CNV detection method called CNproScan focused on bacterial genomes. CNproScan implements a hybrid approach and other bacteria-focused features and depends only on NGS data. We benchmarked our method and compared it to the previously published methods and we can resolve to achieve a higher detection rate together with providing other beneficial features, such as CNV classification. Compared with other methods, CNproScan can detect much shorter CNV events.

Klíčová slova

Next-generation sequencing; Copy number variation; Bacteria; Drug resistance

Klíčová slova v angličtině

Next-generation sequencing; Copy number variation; Bacteria; Drug resistance

Autoři

JUGAS, R.; SEDLÁŘ, K.; VÍTEK, M.; NYKRÝNOVÁ, M.; BARTOŇ, V.; BEZDÍČEK, M.; LENGEROVÁ, M.; ŠKUTKOVÁ, H.

Rok RIV

2022

Vydáno

03.07.2021

Nakladatel

Elsevier

ISSN

0888-7543

Periodikum

GENOMICS

Svazek

113

Číslo

5

Stát

Spojené státy americké

Strany od

3103

Strany do

3111

Strany počet

9

URL

https://www.sciencedirect.com/science/article/abs/pii/S0888754321002779

BibTex

@article{BUT172131,
  author="Robin {Jugas} and Karel {Sedlář} and Martin {Vítek} and Markéta {Jakubíčková} and Vojtěch {Bartoň} and Matěj {Bezdíček} and Martina {Lengerová} and Helena {Vítková}",
  title="CNproScan: Hybrid CNV detection for bacterial genomes
",
  journal="GENOMICS",
  year="2021",
  volume="113",
  number="5",
  pages="3103--3111",
  doi="10.1016/j.ygeno.2021.06.040",
  issn="0888-7543",
  url="https://www.sciencedirect.com/science/article/abs/pii/S0888754321002779"
}