plasmidseeker - identification of known plasmids from whole-genome sequencing reads

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

plasmidseeker 1.0                                 October 2018                                  PLASMIDSEEKER(1)

       plasmidseeker - identification of known plasmids from whole-genome sequencing reads

-i     Input fastq file

       -o     Output file name (default plasmidseeker_result.txt)

       -d     Path to plasmid database directory

       -b     Closest bacteria to isolate genome fna

       -t     Number of threads used (default 32)

       -f     Minimum  threshold  F - at least this fraction of unique k-mers that has to be found for a plasmid
              (default 80)

       -h     Print this help

       --verbose
              Print out more working process

       --ponly
              Assumes that reads contain only plasmid sequences (use for extracted plasmids)

       -v     Print version of the program

plasmidseeker-d<PLASMIDDBDIR>-i<SAMPLE.fastq>-b<CLOSESTBACTERIATOISOLATE>-o<OUTPUTFILE>