scripts/download_script.sh - script to download NCBI bacteria and Archaea references. Also concatenates all references into all_bacteria.fasta / all_archaea.fasta files. Warning: This database is large.
scripts/download_plsdb.sh - script to download and extract the PLSDB plasmid sequences. Note: need to edit the file to change the path to the BLAST+ executables to match your system.
Each script should be run in the directory where you would like to download the files
scripts/filter_plasmids_from_genomes.py - script to create plasmid and genome fastas given single fasta input file
Usage: python filter_plasmids_from_genomes.py -i <input fasta> -p <output plasmid fasta> -f <output genome fasta> [-mn <min length for plasmid (1000)] [-mx <max length for plasmid (1000000)]
scripts/dedup.py - script to remove exact duplicates in a fasta file. e.g. concatenate together the PLSDB fasta file and the plasmids split from refseq into one file and then deduplicate.
Usage: python dedup.py <input fasta> <output fasta>