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date Thu, 19 Oct 2023 12:31:29 +0000
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1 # eurl_vtec_wgs_pt-galaxy
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2 This workflow performs various Escherichia coli typing tools and is implemented as a Galaxy (https://galaxyproject.org/) workflow
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4 Raw data quality check (FASTQC, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
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5 Trimming (Trimmomatic, DOI:10.1093/bioinformatics/btu170)
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6 Assembly (SPAdes, DOI:10.1089/cmb.2012.0021; SKESA, DOI:10.1186/s13059-018-1540-z)
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7 Virulotyping (patho_typing tool from the INNUENDO Project)
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8 Multi Locus Sequence Typing (MLST 7 loci, Seemann T, https://github.com/tseemann/mlst/)
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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)
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10 AMR typing (Abricate, Seemann T, Github https://github.com/tseemann/abricate; ResFinder database DOI:10.1093/jac/dks261)
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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.