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.