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1 # SeqSero 1.0
2 Salmonella serotyping from genome sequencing data
3
4
5 # Introduction
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
7
8 # Dependencies
9 SeqSero depends on:
10
11 1. Python 2.7 and [Biopython 1.65](http://biopython.org/wiki/Download);
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13 2. [Burrows-Wheeler Aligner](http://sourceforge.net/projects/bio-bwa/files/);
14
15 3. [Samtools](http://sourceforge.net/projects/samtools/files/samtools/);
16
17 4. [NCBI BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download);
18
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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21 6. [isPcr](http://hgwdev.cse.ucsc.edu/~kent/exe/linux/) written by Jim Kent.
22
23 # Executing the code
24 Usage: SeqSero.py
25
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)
27
28 -i <file> (/path/to/input/file)
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30 -b <string> (algorithms for bwa mapping; 'mem' for mem, 'sam' for samse/sampe; default=sam; optional)
31
32 # Output
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
34
35 # Citation
36 Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.
37 Salmonella serotype determination utilizing high-throughput genome sequencing data.
38 **J Clin Microbiol.** 2015 May;53(5):1685-92.[PMID:25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15)