Your browser doesn't support javascript.
loading
ToTem: a tool for variant calling pipeline optimization.
Tom, Nikola; Tom, Ondrej; Malcikova, Jitka; Pavlova, Sarka; Kubesova, Blanka; Rausch, Tobias; Kolarik, Miroslav; Benes, Vladimir; Bystry, Vojtech; Pospisilova, Sarka.
Afiliación
  • Tom N; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
  • Tom O; Department of Internal Medicine - Hematology and Oncology, Medical Faculty, Masaryk University and University Hospital Brno, Brno, Czech Republic.
  • Malcikova J; Department of Computer Science, Faculty of Science, Palacky University, Olomouc, Czech Republic.
  • Pavlova S; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
  • Kubesova B; Department of Internal Medicine - Hematology and Oncology, Medical Faculty, Masaryk University and University Hospital Brno, Brno, Czech Republic.
  • Rausch T; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
  • Kolarik M; Department of Internal Medicine - Hematology and Oncology, Medical Faculty, Masaryk University and University Hospital Brno, Brno, Czech Republic.
  • Benes V; Department of Internal Medicine - Hematology and Oncology, Medical Faculty, Masaryk University and University Hospital Brno, Brno, Czech Republic.
  • Bystry V; Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany.
  • Pospisilova S; Department of Computer Science, Faculty of Science, Palacky University, Olomouc, Czech Republic.
BMC Bioinformatics ; 19(1): 243, 2018 06 26.
Article en En | MEDLINE | ID: mdl-29940847
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 .
Asunto(s)
Palabras clave
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Biología Computacional / Secuenciación de Nucleótidos de Alto Rendimiento Idioma: En Revista: BMC Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2018 Tipo del documento: Article País de afiliación: República Checa Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Biología Computacional / Secuenciación de Nucleótidos de Alto Rendimiento Idioma: En Revista: BMC Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2018 Tipo del documento: Article País de afiliación: República Checa Pais de publicación: Reino Unido