ToTem: a tool for variant calling pipeline optimization

Kód výsledku v 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>

Nalezeny alternativní kódy

RIV/00216224:14740/18:00101855 RIV/61989592:15310/18:73588794

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

ToTem: a tool for variant calling pipeline optimization

Popis výsledku v původním jazyce

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&apos;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

Název v anglickém jazyce

ToTem: a tool for variant calling pipeline optimization

Popis výsledku anglicky

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&apos;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

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10609 - Biochemical research methods

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2018

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

BMC Bioinformatics

ISSN

1471-2105

e-ISSN

—

Svazek periodika

19

Číslo periodika v rámci svazku

JUN 2018

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

9

Strana od-do

243

Kód UT WoS článku

000436517200004

EID výsledku v databázi Scopus

2-s2.0-85049074706