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+++ b/SeqSero2/SalmID/README.md	Wed Aug 14 17:45:41 2019 -0400
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+[![DOI](https://zenodo.org/badge/97020646.svg)](https://zenodo.org/badge/latestdoi/97020646)
+
+# 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](http://linuxbrew.sh/) or [MacOS](https://brew.sh/)):
+```
+brew install brewsci/bio/salmid
+```
+Big thanks to [Torsten Seemann](https://tseemann.github.io/) for including this in homebrew!
+
+Alernatively git clone to your machine:
+```
+git clone --recursive https://github.com/hcdenbakker/SalmID.git
+```
+
+Make SalmID executable:
+```
+cd SalmID
+```
+
+```
+chmod +x SalmID.py
+```
+
+
+Add the SalmID folder to your path
+
+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