Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia).
Python 3
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.gitbuild a wheel using poetry:
cd SalmID
poetry buildand install using pip
pip install dist/salmid*.whlTo 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'
- Provide coverage estimates for genomes in sample based on kmer frequencies
- Write code to use SalmID on long read (minion, pacbio) platforms