https://github.com/hcdenbakker/seqsero
Salmonella serotyping from genome sequencing data
Science Score: 10.0%
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Links to: ncbi.nlm.nih.gov -
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Low similarity (7.1%) to scientific vocabulary
Last synced: 6 months ago
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Salmonella serotyping from genome sequencing data
Basic Info
- Host: GitHub
- Owner: hcdenbakker
- License: gpl-2.0
- Language: Python
- Default Branch: master
- Size: 634 KB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Fork of denglab/SeqSero
Created almost 10 years ago
· Last pushed about 10 years ago
https://github.com/hcdenbakker/SeqSero/blob/master/
# 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](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 (input data type, '1' for interleaved paired-end reads , '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly)
-i (/path/to/input/file)
-b (algorithms for bwa mapping; 'mem' for mem, 'sam' for samse/sampe; default=sam; optional)
# Output
Upon executing the command, a directory named 'SeqSero_result_' 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)
Owner
- Name: Henk den Bakker
- Login: hcdenbakker
- Kind: user
- Location: Griffin, GA, USA
- Company: Center for Food Safety, University of Georgia
- Repositories: 7
- Profile: https://github.com/hcdenbakker