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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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ToTem: a tool for variant calling pipeline optimization.

Nikola Tom1,2, Ondrej Tom3, Jitka Malcikova1,2

  • 1Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.

BMC Bioinformatics
|June 27, 2018
PubMed
Summary
This summary is machine-generated.

ToTem automates bioinformatics pipeline optimization for next-generation sequencing (NGS) data. This tool enhances variant calling precision and recall by benchmarking different pipeline settings, ensuring reproducible results.

Keywords:
BenchmarkingNext generation sequencingParameter optimizationVariant calling

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • High-throughput bioinformatics analyses of next-generation sequencing (NGS) data necessitate complex pipeline optimization.
  • Selecting appropriate tools and parameters is crucial for achieving optimal precision and recall in data analysis.

Purpose of the Study:

  • To introduce ToTem, a novel tool for automated bioinformatics pipeline optimization.
  • To provide a user-friendly web application with a graphical user interface (GUI) for streamlining NGS data analysis.

Main Methods:

  • ToTem is a stand-alone Java and PHP web application with a MySQL backend.
  • It automatically generates, executes, and benchmarks various variant calling pipeline configurations.
  • The tool incorporates cross-validation techniques to prevent parameter over-fitting and ensure reproducibility.

Main Results:

  • ToTem facilitates the optimization of somatic variant calling from ultra-deep targeted gene sequencing (TGS) data.
  • It also optimizes germline variant detection in whole genome sequencing (WGS) data.
  • Results are presented via interactive graphs and tables for intuitive selection of optimal pipelines.

Conclusions:

  • ToTem offers an automated solution for optimizing bioinformatics pipelines, improving variant calling accuracy.
  • The tool supports flexibility by allowing integration of various tools and analysis starting points.
  • ToTem is freely available as a web application, promoting wider accessibility for researchers.