Introduction

The rapid growth of DNA sequencing throughput in recent years implies that graphical interfaces for viewing and correcting errors must now handle large numbers of reads, efficiently pinpoint regions of interest and automate as many tasks as possible. We have adapted consed to reflect this. To allow full-feature editing of large datasets while keeping memory requirements low, we developed a viewer, bamScape, that reads billion-read BAM files, identifies and displays problem areas for user review and launches the consed graphical editor on user-selected regions, allowing, in addition to longstanding consed capabilities such as assembly editing, a variety of new features including direct editing of the reference sequence, variant and error detection, display of annotation tracks and the ability to simultaneously process a group of reads. Many batch processing capabilities have been added.The consed package is free to academic, government and non-profit users, and licensed to others for a fee by the University of Washington. The current version (26.0) is available for linux, macosx and solaris systems or as C++ source code. It includes a user's manual (with exercises) and example datasets. http://www.phrap.org/consed/consed.htmldgordon@uw.edu .

Publications

  1. Consed: a graphical editor for next-generation sequencing.
    Cite this
    Gordon D, Green P, 2013-11-01 - Bioinformatics (Oxford, England)
  2. Viewing and editing assembled sequences using Consed.
    Cite this
    Gordon D, 2003-08-01 - Current protocols in bioinformatics

Credits

  1. David Gordon
    Developer

    Department of Genome Sciences, University of Washington, United States of America

  2. Phil Green
    Investigator

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Summary
AccessionBT002251
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByPhil Green