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1 # SeqSero 1.0
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2 Salmonella serotyping from genome sequencing data
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3
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4
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5 # Introduction
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6 SeqSero is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies. A web app is available at www.denglab.info/SeqSero
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7
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8 # Dependencies
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9 SeqSero depends on:
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10
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11 1. Python 2.7 and [Biopython 1.65](http://biopython.org/wiki/Download);
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12
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13 2. [Burrows-Wheeler Aligner](http://sourceforge.net/projects/bio-bwa/files/);
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14
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15 3. [Samtools](http://sourceforge.net/projects/samtools/files/samtools/);
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16
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17 4. [NCBI BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download);
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18
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19 5. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software);
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20
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21 6. [isPcr](http://hgwdev.cse.ucsc.edu/~kent/exe/linux/) written by Jim Kent.
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22
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23 # Executing the code
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24 Usage: SeqSero.py
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25
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26 -m <int> (input data type, '1' for interleaved paired-end reads , '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly)
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27
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28 -i <file> (/path/to/input/file)
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29
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30 -b <string> (algorithms for bwa mapping; 'mem' for mem, 'sam' for samse/sampe; default=sam; optional)
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31
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32 # Output
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33 Upon executing the command, a directory named 'SeqSero_result_<time_you_run_SeqSero>' will be created. Your result will be stored in 'Seqsero_result.txt' in that directory
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34
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35 # Citation
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36 Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.
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37 Salmonella serotype determination utilizing high-throughput genome sequencing data.
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38 **J Clin Microbiol.** 2015 May;53(5):1685-92.[PMID:25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15)
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