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1 [![DOI](https://zenodo.org/badge/97020646.svg)](https://zenodo.org/badge/latestdoi/97020646)
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2
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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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5
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6 ## Requirements:
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7 Python 3
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8
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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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15
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16 Alernatively git clone to your machine:
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17 ```
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18 git clone --recursive https://github.com/hcdenbakker/SalmID.git
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19 ```
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20
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21 Make SalmID executable:
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22 ```
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23 cd SalmID
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24 ```
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25
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26 ```
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27 chmod +x SalmID.py
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28 ```
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29
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30
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31 Add the SalmID folder to your path
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32
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33 To execute:
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34 ```
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35 SalmID.py -e .fastq.gz
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36 ```
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37 This will perform a SalmID run on all fastq.gz files in the current directory.
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38 ```
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39 SalmID.py -i your_fastq_gz.fastq.gz
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40 ```
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41 This will perform a SalmID run on an individual file (i.e., your_fastq_gz.fastq.gz)
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42 ```
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43 SalmID.py -d directory_with_data -e _1.fastq.gz
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44 ```
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45 This will perform a SalmID run on all files in directory 'directory_with_data' with extension '_1.fastq.gz'
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46
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47 ## Todo's and thoughts for future releases:
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48 - Provide coverage estimates for genomes in sample based on kmer frequencies
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49 - Write code to use SalmID on long read (minion, pacbio) platforms
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