jpayne@12: [![DOI](https://zenodo.org/badge/97020646.svg)](https://zenodo.org/badge/latestdoi/97020646)
jpayne@12: 
jpayne@12: # SalmID
jpayne@12: Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia).
jpayne@12: 
jpayne@12: ## Requirements:
jpayne@12: Python 3
jpayne@12: 
jpayne@12: ## Installation:
jpayne@12: The easy way with homebrew ([Linux](http://linuxbrew.sh/) or [MacOS](https://brew.sh/)):
jpayne@12: ```
jpayne@12: brew install brewsci/bio/salmid
jpayne@12: ```
jpayne@12: Big thanks to [Torsten Seemann](https://tseemann.github.io/) for including this in homebrew!
jpayne@12: 
jpayne@12: Alernatively git clone to your machine:
jpayne@12: ```
jpayne@12: git clone --recursive https://github.com/hcdenbakker/SalmID.git
jpayne@12: ```
jpayne@12: 
jpayne@12: Make SalmID executable:
jpayne@12: ```
jpayne@12: cd SalmID
jpayne@12: ```
jpayne@12: 
jpayne@12: ```
jpayne@12: chmod +x SalmID.py
jpayne@12: ```
jpayne@12: 
jpayne@12: 
jpayne@12: Add the SalmID folder to your path
jpayne@12: 
jpayne@12: To execute:
jpayne@12: ```
jpayne@12: SalmID.py -e .fastq.gz
jpayne@12: ```
jpayne@12: This will perform a SalmID run on all fastq.gz files in the current directory.
jpayne@12: ```
jpayne@12: SalmID.py -i your_fastq_gz.fastq.gz
jpayne@12: ```
jpayne@12: This will perform a SalmID run on an individual file (i.e., your_fastq_gz.fastq.gz)
jpayne@12: ```
jpayne@12: SalmID.py -d directory_with_data -e _1.fastq.gz
jpayne@12: ```
jpayne@12: This will perform a SalmID run on all files in directory 'directory_with_data' with extension '_1.fastq.gz'
jpayne@12: 
jpayne@12: ## Todo's and thoughts for future releases:
jpayne@12: - Provide coverage estimates for genomes in sample based on kmer frequencies
jpayne@12: - Write code to use SalmID on long read (minion, pacbio) platforms