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Related Experiment Videos

Hopper: software for automating data tracking and flow in DNA sequencing

T M Smith1, C Abajian, L Hood

  • 1Department of Molecular Biotechnology, University of Washington, Seattle 98195, USA. T.M.Smith, soundbat@u.washington.edu

Computer Applications in the Biosciences : CABIOS
|April 1, 1997
PubMed
Summary
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Automating data handling in large-scale DNA sequencing facilities is crucial. A new Perl program, Hopper, streamlines data processing and quality analysis from sequencers, improving laboratory workflow efficiency.

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Genome-scale DNA sequencing involves complex multistep processes.
  • Large-scale sequencing projects face significant data handling challenges.
  • Current limitations in software hinder systematic tracking of template DNA information and quality monitoring.

Purpose of the Study:

  • To develop automated software tools for managing large-scale DNA sequencing data.
  • To improve the monitoring of laboratory workflow and data quality in sequencing facilities.

Main Methods:

  • Prototyping automation using the UNIX file system for data flow from ABI sequencers.
  • Developing a central Perl program, Hopper, for automated data processing and analysis.

Main Results:

Related Experiment Videos

  • Successful automation of data transfer from sequencers to a data repository.
  • Hopper program automatically analyzes data quality, including read length and base purity.
  • Automated assembly of shotgun sequence data and generation of quality reports.

    • Conclusions:

    • Automated data handling systems are essential for efficient large-scale sequencing.
    • The Hopper program provides a robust solution for data processing and quality control.
    • Streamlined data management enhances the overall quality and productivity of sequencing facilities.