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.

SalmID 0.1.23                                     December 2018                                        SALMID(1)