Determining Optical Mapping Errors by Simulations
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15110%2F21%3A73609650" target="_blank" >RIV/61989592:15110/21:73609650 - isvavai.cz</a>
Alternative codes found
RIV/61989100:27240/21:10248027 RIV/00098892:_____/21:N0000071
Result on the web
<a href="https://academic.oup.com/bioinformatics/article/37/20/3391/6275255" target="_blank" >https://academic.oup.com/bioinformatics/article/37/20/3391/6275255</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1093/bioinformatics/btab259" target="_blank" >10.1093/bioinformatics/btab259</a>
Alternative languages
Result language
angličtina
Original language name
Determining Optical Mapping Errors by Simulations
Original language description
Motivation: Optical mapping is a complementary technology to traditional DNA sequencing technologies, such as next-generation sequencing (NGS). It provides genome-wide, high-resolution restriction maps from single, stained molecules of DNA. It can be used to detect large and small structural variants, copy number variations and complex rearrangements. Optical mapping is affected by different kinds of errors in comparison with traditional DNA sequencing technologies. It is important to understand the source of these errors and how they affect the obtained data. This article proposes a novel approach to modeling errors in the data obtained from the Bionano Genomics Inc. Saphyr system with Direct Label and Stain (DLS) chemistry. Some studies have already addressed this issue for older instruments with nicking enzymes, but we are unaware of a study that addresses this new system. Results: The main result is a framework for studying errors in the data obtained from the Saphyr instrument with DLS chemistry. The framework’s main component is a simulation that computes how major sources of errors for this instrument (a false site, a missing site and resolution errors) affect the distribution of fragment lengths in optical maps. The simulation is parametrized by variables describing these errors and we are using a differential evolution algorithm to evaluate parameters that best fit the data from the instrument. Results of the experiments manifest that this approach can be used to study errors in the optical mapping data analysis.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Result continuities
Project
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Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2021
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
BIOINFORMATICS
ISSN
1367-4803
e-ISSN
1460-2059
Volume of the periodical
37
Issue of the periodical within the volume
20
Country of publishing house
GB - UNITED KINGDOM
Number of pages
7
Pages from-to
3391-3397
UT code for WoS article
000733829400001
EID of the result in the Scopus database
2-s2.0-85134965137