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* Adds install_database.py, the Plassembler database and functionality for mapping plasmid contigs to PLDSB.
* Update the API to -1 and -2 for short reads, matching Unicycler.
* Adds mash as dependency.
* Adds plassembler_top_hits_mash_plsdb.tsv output.
* Adds plasmid_copy_number_short and plasmid_copy_number_long to fasta header for each plasmid.
* Checks dependencies upon initialisation, with message to install Unicycler manually if required.