Sunday, September 1, 2013

Fwd: Consed: A Graphical Editor for Next-Generation Sequencing

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Consed: A Graphical Editor for Next-Generation Sequencing: "

Summary: The rapid growth of DNA sequencing throughput in recent years implies that graphical interfaces for viewing and correcting errors must now handle very 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.

Availability: The consed package is free to academic, government, and nonprofit 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.html

Contact:dgordon@uw.edu

Supplementary information: available at Bioinformatics online

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(Via Bioinformatics - Advance Access.)