Consed - The Contig Editor for Phred-Phrap

Consed is a program for viewing and editing Phrap assemblies. This page gives a brief description of Consed. For information about Phred, Phrap, and Cross_match, please visit www.phrap.com.

Consed was developed by David Gordon in Phil Green's laboratory, and is distributed under license from the University of Washington. Consed is widely used by the largest academic and commercial DNA sequencing laboratories. Consed is available for Linux and Unix, but not for Windows. If you are looking for an easy-to-use contig editor for Windows, we suggest that you check out CodonCode Aligner.

Consed Example Screen Shots

The following screen shots illustrate some of Consed's features.

The image above shows the aligned traces in a contig. Note that:

• The background color indicates the quality of base call, as determined by Phred and Phrap. Light backgrounds correspond to high quality, dark backgrounts to low quality. Black background means that the quality is below a user-definable threshold, or that the part of the read was too low quality to be aligned by Phrap.
• Phrap takes base qualities into account when calculating the contig ("consensus") sequence. In the region shown, only two sequences (A333.r and A612.r) are high quality; however, A612.r has a compression, as identified by Phrap and indicated by the yellow tag.
• Individual sequence traces, or traces for all sequences in this region, can easily be seen by clicking a mouse button:

This picture illustrates how Phred quality scores enable Phrap to do automatically what human "contig editors" used to do - to identify the best sequence (A333.r) in a region with discrepancies, and to base the contig sequence on this sequence.

Consed also offers navigation helps to jump to the next region that needs attention, for example because of low quality consensus sequence or high-quality discrepancies. In addition, Consed can pick primers and finishing reads manually (see picture below) or automatically, and thereby dramatically reduce the time needed to "finish" sequencing projects.

Consed Availability

Consed is available for common Unix platforms, including Mac OS X and Linux (RedHat 7.1.1 or equivalent or newer). Consed is not available for Windows or Classic MacOS. For contig editing on Windows (and Mac OS X), CodonCode Aligner is available and compatible with Phred-Phrap.

Academic users can obtain Consed for restricted academic use free of charge directly from the University of Washington. For details, please visit http://www.phrap.org/consed/consed.html#howToGet.