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preAssemble: a tool for automatic sequencer trace data processing.

Alexei A Adzhubei1, Jon K Laerdahl, Anna V Vlasova

  • 1Norwegian School of Veterinary Science, BasAM-Genetics, PO Box 8146 Dep, NO-0033 Oslo, Norway. a.a.adjoubei@biotek.uio.no

BMC Bioinformatics
|January 19, 2006
PubMed
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preAssemble is a user-friendly pipeline for automatic DNA sequencing quality assessment. It processes chromatogram data efficiently, offering both simple default settings and advanced parameter tuning for various project scales.

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Automatic DNA sequencing generates chromatogram (trace) files containing raw sequencing data.
  • Quality assessment of these trace files is crucial before downstream analysis like clustering and assembly.
  • Existing tools like Phred and Staden are often used for sequence quality processing.

Purpose of the Study:

  • To develop a pipeline for automated, high-throughput processing of DNA sequencer chromatogram data.
  • To provide a user-friendly tool for sequence quality assessment across projects of varying scales.

Main Methods:

  • The preAssemble pipeline integrates the Staden Package Pregap4 module and the Phred base-calling program.
  • It is designed for automatic processing of DNA sequencer chromatogram (trace) data.

Related Experiment Videos

  • The pipeline produces detailed, web-browser-displayable output.

    • Main Results:

    • preAssemble enables automatic processing of DNA sequencer chromatogram data.
    • The pipeline is suitable for small to large-scale sequencing projects.
    • Output is detailed and self-explanatory, viewable via a web browser.

    Conclusions:

    • preAssemble is an effective tool for assessing the quality of automatically generated DNA sequences.
    • It offers flexibility with both a downloadable standalone version and an accessible server-based job submission.
    • The tool is designed for ease of use, requiring minimal prior experience for default operations, while also supporting advanced parameter customization.