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author cstrittmatter
date Mon, 27 Apr 2020 01:11:53 -0400
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1 [![DOI](https://zenodo.org/badge/97020646.svg)](https://zenodo.org/badge/latestdoi/97020646)
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3 # SalmID
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4 Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia).
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6 ## Requirements:
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7 Python 3
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9 ## Installation:
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10 The easy way with homebrew ([Linux](http://linuxbrew.sh/) or [MacOS](https://brew.sh/)):
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11 ```
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12 brew install brewsci/bio/salmid
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13 ```
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14 Big thanks to [Torsten Seemann](https://tseemann.github.io/) for including this in homebrew!
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16 Alternatively download from GitHub:
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18 ```bash
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19 git clone https://github.com/hcdenbakker/SalmID.git
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20 ```
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22 build a wheel using [poetry](https://poetry.eustace.io/):
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24 ```bash
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25 cd SalmID
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26 poetry build
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27 ```
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29 and install using `pip`
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31 ```bash
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32 pip install dist/salmid*.whl
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33 ```
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35 To execute:
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36 ```
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37 SalmID.py -e .fastq.gz
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38 ```
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39 This will perform a SalmID run on all fastq.gz files in the current directory.
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40 ```
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41 SalmID.py -i your_fastq_gz.fastq.gz
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42 ```
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43 This will perform a SalmID run on an individual file (i.e., your_fastq_gz.fastq.gz)
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44 ```
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45 SalmID.py -d directory_with_data -e _1.fastq.gz
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46 ```
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47 This will perform a SalmID run on all files in directory 'directory_with_data' with extension '_1.fastq.gz'
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49 ## Todo's and thoughts for future releases:
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50 - Provide coverage estimates for genomes in sample based on kmer frequencies
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51 - Write code to use SalmID on long read (minion, pacbio) platforms