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Viewing and editing assembled sequences using Consed.

David Gordon1

  • 1Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA.

Current Protocols in Bioinformatics
|April 23, 2008
PubMed
Summary
This summary is machine-generated.

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Consed is a powerful tool for viewing and editing DNA sequence assemblies generated by Phrap. This guide details its features for identifying assembly problems, managing reads, and optimizing sequence data.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Phrap is a widely used program for DNA sequence assembly.
  • Effective visualization and editing tools are crucial for high-quality genome assembly.
  • Consed provides a comprehensive interface for managing and refining Phrap assemblies.

Purpose of the Study:

  • To provide a detailed introduction to the Consed software.
  • To guide users in identifying and resolving issues within DNA sequence assemblies.
  • To outline advanced protocols for assembly refinement and analysis.

Main Methods:

  • Utilizing Consed for viewing and editing Phrap-generated assemblies.
  • Employing Consed's features for problem region identification and searching.

Related Experiment Videos

  • Implementing protocols for read manipulation, primer design, and join correction.
  • Leveraging Consed's integrated tools like Assembly View, Autofinish, and compatibility with PolyPhred.

    • Main Results:

    • Consed facilitates efficient identification of assembly artifacts and errors.
    • Users can effectively manage individual reads and assembly contigs.
    • Advanced features enable primer selection and correction of assembly joins.
    • Integration with Phred and Phrap workflows streamlines the entire assembly process.

    Conclusions:

    • Consed is an indispensable tool for researchers working with Phrap-based DNA sequence assemblies.
    • Mastering Consed enhances the accuracy and reliability of genomic data.
    • The software supports a wide range of tasks from basic viewing to advanced refinement.