Covid Emergency Pipeline
Introduction
The Covid Emergency pipeline allows fast execution of assembly (step_2AS_mapping) and lineage assignment (4TY_lineage) of SARS-CoV2 samples. The reference genome used dutring the mapping step is NC_045512 (Wuhan-Hu-1). Since the tool used for mapping is Snippy, the pipeline also produces the variants' VCF file.
Run Covid Emergency Pipeline
The filter at the top of the run analyses page allows to display only the pipelines. Once the Covid Emergency pipeline has been selected, a confirmation interface will be displayed.
The Covid Emergency pipeline consists of 2 steps:
- Mapping with Snippy (2AS_mapping__snippy);
- Lineage assignment with Pangolin (4TY_lineage__pangolin).
Accepted inputs are the same as for mapping with Snippy, i.e. reads in fastq format:
The input selection UI delivers an advanced input selection mode, to allow selection of all types of supported input files at once.
In the parameter dedicated section it's possible to choose a minimum quality value (20 o 14) for predicted bases, through the field for quality threshold selection.
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 "Covid Emergency" 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:
