add option -ignore-seeds to skip assembly

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
add option -merge-seeds (disabled by default)

This option merges seeds initially to reduce running time.

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>