EXPERIMENT FILES AND THEIR APPLICATION DURING LARGE-SCALE SEQUENCING PROJECTS

The data for large scale sequencing projects are passed through severa l processing steps prior to assembly, and post-assembly processing gen erally requires knowledge of more than just the sequence of each readi ng. We address here the problem of providing data to individual progra ms and of combining all the tasks into a single process. The solution comprises two components: a file format (experiment file format) that stores information about readings, and a script (PREGAP) that controls the creation and use of experiment files by the processing programs. PREGAP can take a batch of data from a variety of sequencing instrumen ts, gather information about each reading, and then scan the reading t o select the 3' end of the good quality data, mark sequencing vector, other cloning vector sequences, and Alu segments. The results of all t hese operations are added to the experiment file for each reading, rea dy for processing by the assembly program. Experiment files also provi de a mechanism for using alternative assembly engines with our package .