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Related Experiment Video

Updated: Jun 12, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification

Joachim M De Schrijver1, Kim De Leeneer, Steve Lefever

  • 1Laboratory for Bioinformatics and Computational Genomics, Department of Molecular Biotechnology, Ghent University, 9000 Ghent, Belgium. Joachim.DeSchrijver@ugent.be

BMC Bioinformatics
|May 22, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces an open-source software pipeline for analyzing next-generation amplicon sequencing data. The tool aids in genetic variation detection and optimizes PCR efficiency for improved sequencing effectiveness.

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Last Updated: Jun 12, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
11:22

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Diagnostics

Background:

  • Next-generation amplicon sequencing facilitates high-throughput genetic diagnostics.
  • Current software solutions lack comprehensive reporting for genetic variations and PCR reaction analysis.

Purpose of the Study:

  • To develop an integrated, open-source software pipeline for analyzing 454/Roche GS-FLX amplicon resequencing data.
  • To enable reliable genetic variation detection, validation, and optimization of PCR efficiency.

Main Methods:

  • Developed a database-oriented software pipeline using Perl and a relational database.
  • Implemented modular design for pipeline customization and integration with other systems.
  • Provided clear documentation and training data for validation.

Main Results:

  • The pipeline enables robust variation detection and validation for amplicon resequencing.
  • Advanced data analysis provides insights for optimizing PCR efficiency.
  • The modular approach allows adaptation to diverse research experiments.

Conclusions:

  • An open-source, database-oriented pipeline for advanced analysis of 454/Roche GS-FLX amplicon resequencing experiments has been created.
  • The modular design facilitates integration with variant interpretation or LIMS systems.
  • Standard reporting scripts are available for enhanced data presentation.