Detail
Článek
Článek online
FT
Medvik - BMČ
  • Je něco špatně v tomto záznamu ?

ToTem: a tool for variant calling pipeline optimization

N. Tom, O. Tom, J. Malcikova, S. Pavlova, B. Kubesova, T. Rausch, M. Kolarik, V. Benes, V. Bystry, S. Pospisilova,

. 2018 ; 19 (1) : 243. [pub] 20180626

Jazyk angličtina Země Anglie, Velká Británie

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/bmc19012590

Grantová podpora
NV15-30015A MZ0 CEP - Centrální evidence projektů
NV15-31834A MZ0 CEP - Centrální evidence projektů

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://totem.software .

Citace poskytuje Crossref.org

000      
00000naa a2200000 a 4500
001      
bmc19012590
003      
CZ-PrNML
005      
20201105114307.0
007      
ta
008      
190405s2018 enk f 000 0|eng||
009      
AR
024    7_
$a 10.1186/s12859-018-2227-x $2 doi
035    __
$a (PubMed)29940847
040    __
$a ABA008 $b cze $d ABA008 $e AACR2
041    0_
$a eng
044    __
$a enk
100    1_
$a Tom, Nikola $u Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic. Department of Internal Medicine - Hematology and Oncology, Medical Faculty, Masaryk University and University Hospital Brno, Brno, Czech Republic.
245    10
$a ToTem: a tool for variant calling pipeline optimization / $c N. Tom, O. Tom, J. Malcikova, S. Pavlova, B. Kubesova, T. Rausch, M. Kolarik, V. Benes, V. Bystry, S. Pospisilova,
520    9_
$a 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://totem.software .
650    _2
$a výpočetní biologie $x metody $7 D019295
650    _2
$a vysoce účinné nukleotidové sekvenování $x metody $7 D059014
650    _2
$a reprodukovatelnost výsledků $7 D015203
650    _2
$a výzkumný projekt $7 D012107
650    _2
$a software $7 D012984
655    _2
$a časopisecké články $7 D016428
655    _2
$a práce podpořená grantem $7 D013485
700    1_
$a Tom, Ondrej $u Department of Computer Science, Faculty of Science, Palacky University, Olomouc, Czech Republic.
700    1_
$a Malcikova, Jitka $u Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic. Department of Internal Medicine - Hematology and Oncology, Medical Faculty, Masaryk University and University Hospital Brno, Brno, Czech Republic.
700    1_
$a Pavlova, Sarka $u Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic. Department of Internal Medicine - Hematology and Oncology, Medical Faculty, Masaryk University and University Hospital Brno, Brno, Czech Republic.
700    1_
$a Kubesova, Blanka $u Department of Internal Medicine - Hematology and Oncology, Medical Faculty, Masaryk University and University Hospital Brno, Brno, Czech Republic.
700    1_
$a Rausch, Tobias $u Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany.
700    1_
$a Kolarik, Miroslav $u Department of Computer Science, Faculty of Science, Palacky University, Olomouc, Czech Republic.
700    1_
$a Benes, Vladimir $u Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany.
700    1_
$a Bystrý, Vojtěch $7 xx0238315 $u Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic. vojtech.bystry@ceitec.muni.cz.
700    1_
$a Pospisilova, Sarka $u Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic. pospisilova.sarka@fnbrno.cz. Department of Internal Medicine - Hematology and Oncology, Medical Faculty, Masaryk University and University Hospital Brno, Brno, Czech Republic. pospisilova.sarka@fnbrno.cz.
773    0_
$w MED00008167 $t BMC bioinformatics $x 1471-2105 $g Roč. 19, č. 1 (2018), s. 243
856    41
$u https://pubmed.ncbi.nlm.nih.gov/29940847 $y Pubmed
910    __
$a ABA008 $b sig $c sign $y a $z 0
990    __
$a 20190405 $b ABA008
991    __
$a 20201105114305 $b ABA008
999    __
$a ok $b bmc $g 1391900 $s 1050895
BAS    __
$a 3
BAS    __
$a PreBMC
BMC    __
$a 2018 $b 19 $c 1 $d 243 $e 20180626 $i 1471-2105 $m BMC bioinformatics $n BMC Bioinformatics $x MED00008167
GRA    __
$a NV15-30015A $p MZ0
GRA    __
$a NV15-31834A $p MZ0
LZP    __
$a Pubmed-20190405
Zpět

Najít záznam

Citační ukazatele

Pouze přihlášení uživatelé

Možnosti archivace