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1 # SeqSero2 alpha-test version
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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 SeqSero2 is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies. This is a alpha test version. For now, it can only accept separated paired-end reads. A web app will be available soon.
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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. [SPAdes](http://bioinf.spbau.ru/spades);
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22
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23 7. [Bedtools](http://bedtools.readthedocs.io/en/latest/).
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24
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25 # Executing the code
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26 Usage: SeqSero2.py
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27
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28 -p <int> (number of threads, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1)
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29
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30 -i <file> (/path/to/input/file; for now, SeqSero2 only accepts separated paired-end reads )
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31
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32 -b <string> (algorithms for bwa mapping; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode)
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33
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34 # Output
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35 Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'Seqsero_result.txt' in that directory. And the assembled alleles can also be found in the directory.
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36
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37 # Citation
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38 Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.
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39 Salmonella serotype determination utilizing high-throughput genome sequencing data.
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40 **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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