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.