jpayne@1: [![DOI](https://zenodo.org/badge/97020646.svg)](https://zenodo.org/badge/latestdoi/97020646)
jpayne@1: 
jpayne@1: # SalmID
jpayne@1: Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia).
jpayne@1: 
jpayne@1: ## Requirements:
jpayne@1: Python 3
jpayne@1: 
jpayne@1: ## Installation:
jpayne@1: The easy way with homebrew ([Linux](http://linuxbrew.sh/) or [MacOS](https://brew.sh/)):
jpayne@1: ```
jpayne@1: brew install brewsci/bio/salmid
jpayne@1: ```
jpayne@1: Big thanks to [Torsten Seemann](https://tseemann.github.io/) for including this in homebrew!
jpayne@1: 
jpayne@1: Alernatively git clone to your machine:
jpayne@1: ```
jpayne@1: git clone --recursive https://github.com/hcdenbakker/SalmID.git
jpayne@1: ```
jpayne@1: 
jpayne@1: Make SalmID executable:
jpayne@1: ```
jpayne@1: cd SalmID
jpayne@1: ```
jpayne@1: 
jpayne@1: ```
jpayne@1: chmod +x SalmID.py
jpayne@1: ```
jpayne@1: 
jpayne@1: 
jpayne@1: Add the SalmID folder to your path
jpayne@1: 
jpayne@1: To execute:
jpayne@1: ```
jpayne@1: SalmID.py -e .fastq.gz
jpayne@1: ```
jpayne@1: This will perform a SalmID run on all fastq.gz files in the current directory.
jpayne@1: ```
jpayne@1: SalmID.py -i your_fastq_gz.fastq.gz
jpayne@1: ```
jpayne@1: This will perform a SalmID run on an individual file (i.e., your_fastq_gz.fastq.gz)
jpayne@1: ```
jpayne@1: SalmID.py -d directory_with_data -e _1.fastq.gz
jpayne@1: ```
jpayne@1: This will perform a SalmID run on all files in directory 'directory_with_data' with extension '_1.fastq.gz'
jpayne@1: 
jpayne@1: ## Todo's and thoughts for future releases:
jpayne@1: - Provide coverage estimates for genomes in sample based on kmer frequencies
jpayne@1: - Write code to use SalmID on long read (minion, pacbio) platforms