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.