In some cases it may be useful to allow ARC to be run for a few more iterations or to resume a run which was terminated for some reason. This could be controlled by adding something to the ARC_config.txt (i.e. restart = True).

Do something like the following:

1. Clean up: old assemblies, intermediate mapping results, and other junk (if any)
2. Check for IX_contigs.fasta where X is range(1, numcycles), choose the last one as the targets to start with (ignore the targets in ARC_config.txt).
3. Set up a Config object with all of the necessary pieces (iteration etc)
4. Run the spawner which should kick off mapping etc effectively resuming the process.