Main tool: PlasmidSeeker
A k-mer based program for the identification of known plasmids from bacterial whole genome sequencing reads
# Identify Plasmids
plasmidseeker.pl -d db_w20 -i ERR1937840.fastq -b e_coli_sakai_ref.fna -o EC_1_results.txt
# Build custom database, with any multifatsa file of plasmids
database_builder.pl -i database.fastas
WARNING!!! You will need to make a database or download one of the databases provided on the github page.
You can also run this wget command: wget http://bioinfo.ut.ee/plasmidseeker/plasmidseeker_db_w20.tar.gz
Then you need to mount the container to with the directory with database. I used this docker command:
docker run -v pwd:pwd -w pwd -i -t plasmidseeker/john plasmidseeker.pl -d /Users/johnarnn/Documents/plasmidseekerdb/db_w20 -i /Users/johnarnn/Documents/plasmidseeker/ERR1937840.fastq -b /Users/johnarnn/Documents/plasmidseeker/e_coli_sakai_ref.fna -o EC_1_results.txt
Better documentation can be found at PlasmidSeeker