4TY_lineage
Introduction
4TY_lineage assigns the lineage of SARS-CoV2 and West Nile Virus. This analysis is specific for such virus.
Run Analysis 4TY_lineage
Once the analysis 4TY_lineage has been selected from the run analyses interface, the user will be able to select which bioinformatic tool to use. The available tools are:
- Pangolin - Phylogenetic Assignment of Named Global Outbreak LINeages
- Westnile - West Nile virus lineage calculation
Pangolin is exclusively for SARS-CoV2 lineage assignment, while Westnile is specific for West Nile Virus.
The input selection UI delivers an advanced input selection mode, to allow selection of all types of supported input files at once.
Accepted inputs can be from:
The tool Westnile only accepts fasta file from 2AS_mapping as input.
4TY_lineage requires input sequences from de novo assembly or mapping; if the latter are provided, the reference genome that has been used for mapping will also be required.
A link to Check analysis will be created after launching the requested analysis. The system will notify the user after a succesful analysis launch and once execution has ended.
Output directory
Please refer to Cohesive's specific Wiki page for information on file download.
The output directory is guida ufficiale di available at the link in the download page or at the link presente in the analysis' summary card, and will have the following structure: results > YEAR > ID > 4TY_lineage > DSXXXXXXXX-DTXXXXXX_pangolin. At that path there will be 2 directories:
- meta: ("metadata") contains log and configuration files.
- result: contains the analysis' output files.
Pangolin
| File | Description | Location |
|---|---|---|
| DSXXXXXXXX-DTXXXXXX_ID_pangolin_lineage_report.csv | csv file with assigned lineage | result directory |
Westnile
| File | Description | Location |
|---|---|---|
| DSXXXXXXXX-DTXXXXXX_ID_westnile_lineage.csv | csv file with assigned lineage | result directory |
| DSXXXXXXXX-DTXXXXXX_ID_westnile_lineage_summary.csv | csv summary table | result directory |
