Mercurial > repos > cstrittmatter > test_galtrakr_eurl_vtec_wgs_pt_23
comparison README.md @ 0:8be2feb96994
"planemo upload commit cb65588391944306ff3cb32a23e1c28f65122014"
| author | cstrittmatter |
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| date | Fri, 11 Mar 2022 15:50:35 -0500 |
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| 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 | |
| 3 | |
| 4 Raw data quality check (FASTQC, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | |
| 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) | |
| 7 Virulotyping (patho_typing tool from the INNUENDO Project) | |
| 8 Multi Locus Sequence Typing (MLST 7 loci, https://github.com/tseemann/mlst/) | |
| 9 Serotyping (MMseqs2, DOI:10.1038/s41467-018-04964-5) | |
| 10 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) | |
| 11 AMR typing (AMRFinderPlus, DOI:10.1128/aac.00483-19) | |
| 12 | |
| 13 After installation the BASE_URL parameter in the EURL_VTEC_WGS_PT.py (line 20) will have to be modified to the url of your Galaxy instance in order to correctly visualise the FastQC results. | |
| 14 | |
| 15 The files duk, fastq_pair, stx_subtype_fa.sh, stx_subtype_pe.sh, stx_subtype_se.sh in the scripts folder and the file rematch.py in the scripts/ReMatCh folder should have execution rights. | |
| 16 | |
| 17 In order to make trimmomatic work, you will have to create the following symbolic link | |
| 18 | |
| 19 cd /$GALAXY_DIR/tool_dependency_dir/_conda/envs/mulled-v1-9471dd12387e90c11124403c650a667dc2a8c932d610ab6fc4cf2e3f4b40720c/bin | |
| 20 chmod 755 ../share/trimmomatic-0.39-1/trimmomatic.jar | |
| 21 ln -s ../share/trimmomatic-0.39-1/trimmomatic.jar trimmomatic.jar |