Chris Abajian, David Gordon, Leroy Hood, Phil Green.
Department of Molecular Biotechnology, University of Washington, Seattle WA
Two approaches to reducing the cost of finishing shotgun sequence assemblies are 1) improving the quality of the initial computer-generated assembly, reducing the amount of human intervention required and 2) optimizing the user interface to maximize efficiency of the finisher's effort. Phil Green has written an assembly program, Phrap, that performs very well compared to other commonly-used assembly programs but does not provide for editing or graphical display of the assembly. Consed ("CONSensus Editor") is a graphical editing tool that allows users to view and edit the output of Phrap. It takes advantage of Phrap's assembly algorithm and provides an editing interface designed in collaboration with experienced finishers in the department. Consed is written in C++ and is supported on a variety of platforms, including Solaris, SunOs, HP-UX and OSF- 1.