SalmID

Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia).

Requirements:

Python 3

Installation:

The easy way with homebrew (Linux or MacOS):

brew install brewsci/bio/salmid

Big thanks to Torsten Seemann for including this in homebrew!

Alternatively download from GitHub:

git clone https://github.com/hcdenbakker/SalmID.git

build a wheel using poetry:

cd SalmID
poetry build

and install using pip

pip install dist/salmid*.whl

To execute:

SalmID.py -e .fastq.gz

This will perform a SalmID run on all fastq.gz files in the current directory.

SalmID.py -i your_fastq_gz.fastq.gz

This will perform a SalmID run on an individual file (i.e., your_fastq_gz.fastq.gz)

SalmID.py -d directory_with_data -e _1.fastq.gz

This will perform a SalmID run on all files in directory 'directory_with_data' with extension '_1.fastq.gz'

Todo's and thoughts for future releases:

Provide coverage estimates for genomes in sample based on kmer frequencies
Write code to use SalmID on long read (minion, pacbio) platforms