Unix file system organization for the sequence preprocessor package. Raw DNA fragment trace files, organized by gel (gel folders), are inputs for the preprocessor. Processed reads suitable for assembly are written to disk in the appropriate sequencing project directories. Further structure is created automatically within projects by the software as needed. For example, reads that were successfully processed but contain unusable data, e.g. vector sequences, are placed in a Failures directory. Reads that could not be processed, such as cases in which the trace file contains no data, are put into an Abandoned directory. The Logs directory holds all the indexed summaries and text-based log files; the Qstats directory contains base quality statistics files. This arrangement maintains a convenient division for files of various types.
