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# GalaxySeqSero
#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.

All below dependencies are the same for Seqsero.
 Add this project to the galaxy tools directory and then added to tool_conf.xml

Adding custom tools to Galaxy

https://galaxyproject.org/admin/tools/add-tool-tutorial/


# SeqSero 1.1
Salmonella serotyping from genome sequencing data


# Introduction 
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 

# Dependencies 
SeqSero depends on:

1. Python 2.7 and [Biopython 1.65](http://biopython.org/wiki/Download); 

2. [Burrows-Wheeler Aligner](http://sourceforge.net/projects/bio-bwa/files/); 

3. [Samtools](http://sourceforge.net/projects/samtools/files/samtools/);

4. [NCBI BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download);

5. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software);

6. [isPcr](http://hgwdev.cse.ucsc.edu/~kent/exe/linux/) written by Jim Kent. 

# Executing the code 
    Usage: SeqSero.py 

    -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) 

    -i <file> (/path/to/input/file) 

    -b <string> (algorithms for bwa mapping; 'mem' for mem, 'sam' for samse/sampe; default=sam; optional) 

# Output 
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

# Citation
Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.  
Salmonella serotype determination utilizing high-throughput genome sequencing data.  
**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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# GalaxySeqSero
GalaxySeqSero
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