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Salmonella serotyping from genome sequencing data
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README.md

SeqSero

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;

  2. Burrows-Wheeler Aligner;

  3. Samtools;

  4. NCBI BLAST;

  5. SRA Toolkit;

  6. isPcr 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

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