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SangeR: the high-throughput Sanger sequencing analysis pipeline.

Kai Schmid1, Hildegard Dohmen1, Nadja Ritschel1

  • 1Department of Neuropathology, Justus-Liebig University Giessen, Arndtstr, 16 D-35392 Giessen, Germany.

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Summary

This study introduces SangeR, a high-throughput pipeline for Sanger sequencing analysis, automating variant verification and providing binary mutation calls for genetic analysis. It simplifies complex data, making Sanger sequencing more efficient for various research applications.

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Area of Science:

  • Genetics
  • Bioinformatics
  • Molecular Biology

Background:

  • The Sanger sequencing technique remains crucial for variant verification and targeted genetic analysis despite advancements in high-throughput sequencing.
  • Current Sanger sequencing analysis often requires significant manual intervention, leading to time-consuming workflows.

Purpose of the Study:

  • To develop a high-throughput, automated pipeline for Sanger sequencing data analysis.
  • To provide a binary mutation decision for specific genetic hotspots.
  • To offer an optional web interface for enhanced usability and visualization.

Main Methods:

  • Development of a pipeline-capable software solution named SangeR.
  • Integration of an optional Shiny web interface for user interaction.
  • Processing of Sanger sequencing data to generate binary mutation calls and annotated chromatogram plots.

Main Results:

  • SangeR successfully automates the analysis of Sanger sequencing data, reducing manual effort.
  • The pipeline provides clear binary mutation decisions for targeted genetic analysis.
  • Annotated chromatogram plots are generated for visual inspection and verification.

Conclusions:

  • SangeR offers an efficient, high-throughput solution for Sanger sequencing analysis, suitable for variant verification and genetic studies.
  • The software streamlines data interpretation and facilitates low-cost molecular genetic analysis.
  • SangeR is freely available, promoting wider adoption in research settings.