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author iss
date Tue, 22 Mar 2022 08:39:10 +0000
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1 # eurl_vtec_wgs_pt-galaxy 1 # eurl_vtec_wgs_pt-galaxy
2 This tool performs various Escherichia coli typing tools and is implemented as a Galaxy (https://galaxyproject.org/) workflow 2 This workflow performs various Escherichia coli typing tools and is implemented as a Galaxy (https://galaxyproject.org/) workflow
3 3
4 Raw data quality check (FASTQC, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) 4 Raw data quality check (FASTQC, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
5 Trimming (Trimmomatic, DOI:10.1093/bioinformatics/btu170) 5 Trimming (Trimmomatic, DOI:10.1093/bioinformatics/btu170)
6 Assembly (SPAdes, DOI:10.1089/cmb.2012.0021; SKESA, DOI:10.1186/s13059-018-1540-z) 6 Assembly (SPAdes, DOI:10.1089/cmb.2012.0021; SKESA, DOI:10.1186/s13059-018-1540-z)
7 Virulotyping (patho_typing tool from the INNUENDO Project) 7 Virulotyping (patho_typing tool from the INNUENDO Project)
8 Multi Locus Sequence Typing (MLST 7 loci, Seemann T, https://github.com/tseemann/mlst/) 8 Multi Locus Sequence Typing (MLST 7 loci, Seemann T, https://github.com/tseemann/mlst/)
9 Shigatoxintyping (blastn, DOI:10.1186/1471-2105-10-421, of a consensus sequence against the shiga toxin subtype database from the Statens Serum Institut SSI and Technical University of Denmark DTU, DOI:10.1128/JCM.00008-15) 9 Shigatoxintyping (blastn, DOI:10.1186/1471-2105-10-421, of a consensus sequence against the shiga toxin subtype database from the Statens Serum Institut SSI and Technical University of Denmark DTU, DOI:10.1128/JCM.00008-15)
10 AMR typing (Abricate, Seemann T, Github https://github.com/tseemann/abricate; ResFinder database DOI:10.1093/jac/dks261) 10 AMR typing (Abricate, Seemann T, Github https://github.com/tseemann/abricate; ResFinder database DOI:10.1093/jac/dks261)
11 11
12 After installation the BASE_URL parameter in the EURL_VTEC_WGS_PT.py file (line 20) will have to be modified to the url of your Galaxy instance in order to correctly visualise the FastQC results. 12 The value of `galaxy_infrastructure_url` in the galaxy.yml file has to be set to the url of your Galaxy instance in order to correctly visualise the FastQC and AMR results.