The Processes Performed

The pregap stages are as follows:

1. General initialisation
   • Process the $PREGAPROOT/system-pregaprc file.
   • Process $HOME/.pregaprc (if it exists)
   • Process ./.pregaprc (if it exists)
   • Ask the user for input on any questions we still do not have the answers to.
   • Remove or truncate any temporary files we'll be using.

2. Convert the raw trace file to an SCF file.
   • Obtain the sample name from the trace file (to decide upon filenames to use for the Experiment and SCF files)
   • Use 'makeSCF' to produce the SCF file. Not required for PLN or SCF input file formats.

3. Estimate Base Accuracies.
   • The 'eba' program.

4. Create experiment files.
   • The 'init_exp' program

5. Augment the experiment files.
   • For each defined Experiment file line type we evaluate the associated command or utilise the associated variable to create the relevant experiment file line.

6. Perform quality clipping (optional).
   • The 'clip' program which works on the called bases.

   The flow of data through the pregap stages. The input file formats are shown at the top along with any necessary conversion stages. The dotted arrows show paths to skip the optional stages.

7. Perform vector clipping (optional).
   • Sequence vector - use 'vepe' option 1.
   • Cloning vector - use 'vepe' option 2.

8. Perform interactive quality clipping (optional).
   • Interactive clipping using the 'trev' program.

9. Screen against vector (optional).
   • Vector rearrangements - use 'vepe' option 3.

10. Tag repeat segments (optional).
    • The 'repe' program.

11. Final preparations.
    • Explain the files created to the user.