Consed: a graphical tool for sequence finishing

Sequencing of large clones or small genomes is generally done by the shotgun approach Although complete automation of data processing in shotgun sequencing is clearly desirable and may be feasible in the near future, at present finishing still requires extensive human intervention. This is customarily done by use of an interactive computer program. The program (which is usually called a sequence editor) must, at a minimum, display the aligned sequences of the assembled reads and allow the user to access underlying raw data (e.g., the fluorescence trace profiles from automated sequencers) and other information that may be useful in evaluating the base calls and assembly. It should also facilitate the detection of regions where additional data are needed, help in determining reagents (e.g., sequencing primers and templates) needed to obtain these data, and allow editing to correct errors. A good editor makes the finishing process as efficient and painless as possible. The display should indicate, with appropriate size and color emphases, the most important information about the assembly, with less important information being easily accessible with a minimum of effort, and the user should have the ability to change which information is shown, on the basis of the task at hand. Locations requiring human inspection should be efficiently pinpointed. The user manipulations required to accomplish a given task should be as natural and efficient as possible. The program should allow customization to suit individual preferences, facilitate quick detection and correction of user mistakes, and be easy to learn. It should have a quick response time and allow recovery from hardware and software problems on the users's computer. A number of editors are available commercially or from academic developers. The pioneering work in both assembly and editing was done by Staden, and his gap4 program We have developed an editor consed that is intended to be used in conjunction with several other sequence data processing programs developed by our group, including the base-calling program phre