plasmidseeker1
Identification of known plasmids from whole-genome sequencing reads
Usage
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