Science Score: 10.0%
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Low similarity (8.2%) to scientific vocabulary
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SeqSero2 alpha test
Basic Info
- Host: GitHub
- Owner: hcdenbakker
- License: gpl-2.0
- Language: Python
- Default Branch: master
- Size: 175 KB
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- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Fork of denglab/SeqSero2
Created over 8 years ago
· Last pushed over 8 years ago
https://github.com/hcdenbakker/SeqSero2/blob/master/
# SeqSero2 alpha-test version
Salmonella serotyping from genome sequencing data
# Introduction
SeqSero2 is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies. This is a alpha test version. For now, it can only accept separated paired-end reads. A web app will be available soon.
# 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. [SPAdes](http://bioinf.spbau.ru/spades);
7. [Bedtools](http://bedtools.readthedocs.io/en/latest/).
# Executing the code
Usage: SeqSero2.py
-p (number of threads, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1)
-i (/path/to/input/file; for now, SeqSero2 only accepts separated paired-end reads )
-b (algorithms for bwa mapping; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode)
# Output
Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'Seqsero_result.txt' in that directory. And the assembled alleles can also be found in the 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