plasmidseeker(1)

identification of known plasmids from whole-genome sequencing reads

Section 1 plasmidseeker bookworm source

Description

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

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

	-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

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