NAME

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

SYNOPSIS

       plasmidseeker -d <PLASMID DB DIR> -i <SAMPLE.fastq> -b <CLOSEST BACTERIA TO ISOLATE> -o <OUTPUT FILE>

OPTIONS

       -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

AUTHOR

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