hcdenbakker / SalmID

Rapid confirmation of Salmonella spp. and subspp. from sequence data

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