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2 # GalaxySeqSero
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3 #This Project has been modified by the CFSAN FDA office to work in Galaxy it also has a batch functionality as well add by the Galaxy rapper code.
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5 All below dependencies are the same for Seqsero.
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6 Add this project to the galaxy tools directory and then added to tool_conf.xml
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8 Adding custom tools to Galaxy
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10 https://galaxyproject.org/admin/tools/add-tool-tutorial/
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13 # SeqSero 1.1
0
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14 Salmonella serotyping from genome sequencing data
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17 # Introduction
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18 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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20 # Dependencies
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21 SeqSero depends on:
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23 1. Python 2.7 and [Biopython 1.65](http://biopython.org/wiki/Download);
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25 2. [Burrows-Wheeler Aligner](http://sourceforge.net/projects/bio-bwa/files/);
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27 3. [Samtools](http://sourceforge.net/projects/samtools/files/samtools/);
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29 4. [NCBI BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download);
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31 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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33 6. [isPcr](http://hgwdev.cse.ucsc.edu/~kent/exe/linux/) written by Jim Kent.
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35 # Executing the code
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36 Usage: SeqSero.py
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38 -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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40 -i <file> (/path/to/input/file)
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42 -b <string> (algorithms for bwa mapping; 'mem' for mem, 'sam' for samse/sampe; default=sam; optional)
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44 # Output
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45 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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47 # Citation
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48 Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.
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49 Salmonella serotype determination utilizing high-throughput genome sequencing data.
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50 **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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51 =======
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52 # GalaxySeqSero
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53 GalaxySeqSero
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54 >>>>>>> 99716906dbfd51e33c03185441d7af761d5f74b2