Detailed Information on Publication Record
2018
ToTem: a tool for variant calling pipeline optimization
TOM, Nikola, O. TOM, Jitka MALČÍKOVÁ, Šárka PAVLOVÁ, Blanka KUBEŠOVÁ et. al.Basic information
Original name
ToTem: a tool for variant calling pipeline optimization
Authors
TOM, Nikola (203 Czech Republic, belonging to the institution), O. TOM (203 Czech Republic), Jitka MALČÍKOVÁ (203 Czech Republic, belonging to the institution), Šárka PAVLOVÁ (203 Czech Republic, belonging to the institution), Blanka KUBEŠOVÁ (203 Czech Republic, belonging to the institution), T. RAUSCH (276 Germany), M. KOLARIK (203 Czech Republic), V. BENES (276 Germany), Vojtěch BYSTRÝ (203 Czech Republic, belonging to the institution) and Šárka POSPÍŠILOVÁ (203 Czech Republic, guarantor, belonging to the institution)
Edition
BMC Bioinformatics, London, BioMed Central, 2018, 1471-2105
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10608 Biochemistry and molecular biology
Country of publisher
United Kingdom of Great Britain and Northern Ireland
Confidentiality degree
není předmětem státního či obchodního tajemství
References:
Impact factor
Impact factor: 2.511
RIV identification code
RIV/00216224:14740/18:00101855
Organization unit
Central European Institute of Technology
UT WoS
000436517200004
Keywords in English
Variant calling; Benchmarking; Next generation sequencing; Parameter optimization
Tags
International impact, Reviewed
Změněno: 13/3/2019 17:22, Mgr. Pavla Foltynová, Ph.D.
Abstract
V originále
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
Links
| EF16_013/0001818, research and development project |
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| LM2015064, research and development project |
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| LQ1601, research and development project |
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| MUNI/A/0968/2017, interní kód MU |
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| NV15-30015A, research and development project |
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| NV15-31834A, research and development project |
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| TE02000058, research and development project |
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| 692298, interní kód MU |
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