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| SALMID(1) |
User Commands |
SALMID(1) |
NAME¶
SalmID - rapid Kmer based Salmonella identifier from sequence data
SYNOPSIS¶
SalmID [-h] [-v] [-i your_fastqgz] [-e file_extension] [-d directory] [-r
percentage, coverage or taxonomy] [-m quick or thorough]
DESCRIPTION¶
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).
OPTIONS¶
- -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
AUTHOR¶
This manpage was written by Andreas Tille for the Debian distribution and can be
used for any other usage of the program.
