Finally, the GS De Novo Assembler and GS Reference Mapper applications create a “Post-Run Analysis” sub-directory to include all the files they generate, using the following naming convention:
The rest of the files within these directories (or within the current working directory) have either fixed names or simple, standard naming conventions (e.g. files specific to a region or key are named with the region or key at the beginning of the name). Exact nomenclature for all the files and other sub-folders produced by the data processing applications are provided in the “output” subsection of the description of each application, in the various Sections of Parts A, B, C, and D of this manual.
