NgsManager Pipeline
NOTE: some of the NgsManager pipeline's components are not yet implemented in Cohesive Demo's current version.
Introduction
The NgsManager pipeline manages reads and executes subordinate pipelines depending on the sample type.
Run NgsManager Pipeline
The filter at the top of the run analyses page allows to display only the pipelines. Once the NgsManager pipeline has been selected, a confirmation interface will be displayed.
Depending on sample type, NgsManager can execute the following pipelines:
- Raw Reads Processing
- For bacteria:
- WGS on Bacteria
- Typing on Bacteria
- For viruses:
- Vdraft pipeline
- For SARS-CoV2:
(For more information on single analyses, please refer to the corresponding pages, available from the list above).
NgsManager's pipeline selection is controlled by choosing the appropriate sample type among the 3 available in the Parameters section.
Accepted inputs are:
- raw reads
- fasta from mapping (step_2AS_mapping)
In case 2AS_mapping is selected as input, NgsManager will also require the reference genome that has been used for mapping. The Raw Reads Processing pipeline will be executed on any sample type, provided that raw reads are used as input.
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 "NgsManager" pipeline depend on the constituent pipelines that are executed, and are organized in the same directory structure. For details on the pipeline's output files, please refer to the output sections of the appropriate analyses:
- Results of the pipeline for bacteria:
- Results of the pipeline "WGS su Batteri"
- Results of the pipeline "Typing su batteri"
- Results of the pipeline "Vdraft" for viruses
- Results of the pipeline "Covid Emergency" for SARS-CoV2
