SalmID - rapid Kmer based Salmonella identifier from sequence data
SalmID [-h] [-v] [-i your_fastqgz] [-e file_extension] [-d directory] [-r
percentage, coverage or taxonomy] [-m quick or thorough]
SalmID enables rapid confirmation of Salmonella spp. and subspp. from sequence
data. This is done by checking taxonomic ID of single isolate samples.
Currently only IDs Salmonella species and subspecies, and some common
contaminants (Listeria, Escherichia).
-
-h, --help
- show this help message and exit
-
-v, --version
- show program's version number and exit
-
-i your_fastqgz, --input_file
your_fastqgz
- Single fastq.gz file input, include path to file if file is
not in same directory
-
-e file_extension, --extension
file_extension
- File extension, if specified without
"--input_dir", SalmID will attempt to ID all files with this
extension in current directory, otherwise files in input directory
-
-d directory, --input_dir directory
- Directory which contains data for identification, when not
specified files in current directory will be analyzed.
-
-r percentage, coverage or taxonomy, --report
percentage, coverage or taxonomy
- Report either percentage ("percentage") of clade
specific kmers recovered, average kmer-coverage ("cov"), or
taxonomy (taxonomic species ID, plus observed mean k-mer coverages and
expected coverage).
-
-m quick or thorough, --mode quick or
thorough
- Quick [quick] or thorough [thorough] mode
This manpage was written by Andreas Tille for the Debian distribution and can be
used for any other usage of the program.