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.