ToTem: a tool for variant calling pipeline optimization
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F65269705%3A_____%2F18%3A00068775" target="_blank" >RIV/65269705:_____/18:00068775 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14740/18:00101855 RIV/61989592:15310/18:73588794
Result on the web
<a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2227-x" target="_blank" >https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2227-x</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1186/s12859-018-2227-x" target="_blank" >10.1186/s12859-018-2227-x</a>
Alternative languages
Result language
angličtina
Original language name
ToTem: a tool for variant calling pipeline optimization
Original language description
Background: High-throughput bioinformatics analyses of next generation sequencing (NGS) data often require challenging pipeline optimization. The key problem is choosing appropriate tools and selecting the best parameters for optimal precision and recall. Results: Here we introduce ToTem, a tool for automated pipeline optimization. ToTem is a stand-alone web application with a comprehensive graphical user interface (GUI). ToTem is written in Java and PHP with an underlying connection to a MySQL database. Its primary role is to automatically generate, execute and benchmark different variant calling pipeline settings. Our tool allows an analysis to be started from any level of the process and with the possibility of plugging almost any tool or code. To prevent an over-fitting of pipeline parameters, ToTem ensures the reproducibility of these by using cross validation techniques that penalize the final precision, recall and F-measure. The results are interpreted as interactive graphs and tables allowing an optimal pipeline to be selected, based on the user's priorities. Using ToTem, we were able to optimize somatic variant calling from ultra-deep targeted gene sequencing (TGS) data and germline variant detection in whole genome sequencing (WGS) data. Conclusions: ToTem is a tool for automated pipeline optimization which is freely available as a web application at https://totern.software
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
10609 - Biochemical research methods
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2018
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
BMC Bioinformatics
ISSN
1471-2105
e-ISSN
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Volume of the periodical
19
Issue of the periodical within the volume
JUN 2018
Country of publishing house
GB - UNITED KINGDOM
Number of pages
9
Pages from-to
243
UT code for WoS article
000436517200004
EID of the result in the Scopus database
2-s2.0-85049074706