Scroll to navigation
| PLASMIDSEEKER(1) |
User Commands |
PLASMIDSEEKER(1) |
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.
