Order and orient
This tool tries to order and orient the contigs of a genome using a reference. It is based on the libraries of : https://github.com/jasperlinthorst/reveal
python assembly_finishing.py --minmum minimal_match_size -n number_of_N_to_insert_between_contigs reference.fasta contigs.fasta
optional : -discard don't append the contigs that couldn't be ordered and orientated to the output -p prune all sequences of N to a single N (overrides the -n option), even those present in the input contigs