SalmID(1)

Usage

SalmID [-h] [-v] [-i your_fastqgz] [-e file_extension] [-d directory] [-r percentage, coverage or taxonomy] [-m quick or thorough]

Overview

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

Releases

Unchanged in 4 releases since Debian 10 (Buster).

10–13