---
name: "SalmID"
section: "1"
platform: "linux"
package: "salmid"
version: "0.1.23-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/SalmID"
---

# SalmID(1)

rapid Kmer based Salmonella identifier from sequence data

## 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.