Pipeline Typing on Bacteria
NOTE: some of the Typing on Bacteria pipeline's components are not yet implemented in Cohesive Demo's current version.
Introduction
The pipeline Typing on Bacteria executes all typing analyses for bacteria, including:
- calculation of species ;
- identification of antibiotic resistance- and virulence-related genes;
- identification of flaA locus variant (Campylobacter only);
- MLST;
- core-genome MLST;
- whole-genome MLST;
- genome annotation;
- calculation of horizontal and vertical coverage.
Run Typing on Bacteria Pipeline
The filter at the top of the run analyses page allows to display only the pipelines. Once the Typing on Bacteria pipeline has been selected, a confirmation interface will be displayed.
The pipeline consists of the following analyses:
Sui risultati di kmerfinder (3TX_species) vengono inoltre eseguite:
The software used for 4TY_cgMLST and 4TY_wgMLST is selected based on the schemas for microorganisms that are available for each tool, as explained in the appropriate Wiki pages:
Similarly, 4TY_MLST_mlst is executed only if the appropriate microorganism schema is available (the full list of schemas is accessible at the official mlst guide on GitHub), 4TY_flaA is only executed on Campylobacter samples and 4TY_cgMLST_mentalist on trimmed reads is only executed in case of Listeria monocytogenes samples.
Accepetd inputs are consensus sequences (.fasta format) obtained from mapping (2AS_mapping) or scaffolds from de novo assembly (2AS_denovo).
In case 2AS_mapping is selected as input, the pipeline will also require a reference genome among those available.
The input selection UI delivers an advanced input selection mode, to allow selection of all types of supported input files at once.
A link to Check analysis will be created after launching the requested pipeline. The system will notify the user after a succesful pipeline launch and once execution has ended.
Results
Output files from the "Typing on Bacteria" pipeline are the same as those produced by the single analyses included in it, in the same directory structure. For details on the pipeline's output files, please refer to the output sections of the appropriate analyses:
- Output of species assignment
- Output of antibiotic-resistance and virulence prediction
- Output per la determinazione della variante del locus flaA
- Output of Multi-Locus Sequence Typing (MLST)
- Output of core-genome MLST (cgMLST)
- Output of whole-genome MLST (wgMLST)
- Output of genome annotation
- Output of mapping on kmerfinder's results
