Enterotoxin S. aureus Finder Pipeline
Introduction
The Enterotoxin Staphylococcus aureus Finder pipeline detects the gene coding for enterotoxin in the genome of S. aureus, running first the de novo assembly (2AS_denovo), followed by typing 4AN_AMR.
Run Enterotoxin S. aureus Finder Pipeline
The filter at the top of the run analyses page allows to display only the pipelines. Once the Enterotoxin S. aureus Finder pipeline has been selected, a confirmation interface will be displayed.
The pipeline performs the following 2 analyses:
- de novo assembly with Unicycler (2AS_denovo__unicycler)
- detection of enterotoxin-coding gene with blast (4AN_AMR__blast)
Accepted inputs can be from pre-processing analyses:
- depleted reads (step_1PP_hostdepl)
- downsampled reads (step_1PP_downsampling)
- trimmed reads (step_1PP_trimming)
- filtered reads (step_1PP_filtering)
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 "Enterotoxin S. aureus Finder" pipeline are the same as those produced by the single analyses included in it, in the same directory structure:
