| TOM, Nikola, O. TOM, Jitka MALČÍKOVÁ, Šárka PAVLOVÁ, Blanka KUBEŠOVÁ, T. RAUSCH, M. KOLARIK, V. BENES, Vojtěch BYSTRÝ and Šárka POSPÍŠILOVÁ. ToTem: a tool for variant calling pipeline optimization. BMC Bioinformatics. London: BioMed Central, 2018, vol. 19, JUN, p. 243-251. ISSN 1471-2105. Available from: https://dx.doi.org/10.1186/s12859-018-2227-x. |
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@article{1443180,
author = {Tom, Nikola and Tom, O. and Malčíková, Jitka and Pavlová, Šárka and Kubešová, Blanka and Rausch, T. and Kolarik, M. and Benes, V. and Bystrý, Vojtěch and Pospíšilová, Šárka},
article_location = {London},
article_number = {JUN},
doi = {http://dx.doi.org/10.1186/s12859-018-2227-x},
keywords = {Variant calling; Benchmarking; Next generation sequencing; Parameter optimization},
language = {eng},
issn = {1471-2105},
journal = {BMC Bioinformatics},
title = {ToTem: a tool for variant calling pipeline optimization},
url = {https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2227-x},
volume = {19},
year = {2018}
}
TY - JOUR
ID - 1443180
AU - Tom, Nikola - Tom, O. - Malčíková, Jitka - Pavlová, Šárka - Kubešová, Blanka - Rausch, T. - Kolarik, M. - Benes, V. - Bystrý, Vojtěch - Pospíšilová, Šárka
PY - 2018
TI - ToTem: a tool for variant calling pipeline optimization
JF - BMC Bioinformatics
VL - 19
IS - JUN
SP - 243
EP - 243
PB - BioMed Central
SN - 14712105
KW - Variant calling
KW - Benchmarking
KW - Next generation sequencing
KW - Parameter optimization
UR - https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2227-x
N2 - 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
ER -
TOM, Nikola, O. TOM, Jitka MALČÍKOVÁ, Šárka PAVLOVÁ, Blanka KUBEŠOVÁ, T. RAUSCH, M. KOLARIK, V. BENES, Vojtěch BYSTRÝ and Šárka POSPÍŠILOVÁ. ToTem: a tool for variant calling pipeline optimization. \textit{BMC Bioinformatics}. London: BioMed Central, 2018, vol.~19, JUN, p.~243-251. ISSN~1471-2105. Available from: https://dx.doi.org/10.1186/s12859-018-2227-x.
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