WNV (West Nile Virus) Pipeline
Introduction
The "WNV - Lineage Calculation and Mapping" pipeline computes lineage for West Nile Virus maps the sample to the appropriate reference.
Run WNV Pipeline
The filter at the top of the run analyses page allows to display only the pipelines. Once the WNV pipeline has been selected, a confirmation interface will be displayed.
The WNV pipeline consists of 2 steps:
- West Nile Virus lineage computation with Westnile (4TY_lineage__westnile);
- Mapping of all the provided genome fragments with Ivar (2AS_mapping__ivar), using multiple references.
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.
The reference genome used for mapping will be the base genome corresponding to the lineage assigned by the Westnile tool, following the relationships in the table below:
| assigned lineage | reference |
|---|---|
| lin. 1 | FJ483548.1 |
| lin. 2 | HQ537483.1 |
| lin. 3 | AY765264.1 |
| lin. 4 | AY277251.1 |
| lin. 5 | GQ851605.1 |
| lin. 6 | GU047875.1 |
| lin. 7 | KY703855.1 |
| lin. 8 | KY703856.1 |
| lin. 9 | KJ831223.1 |
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 "WNV" 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:
