Type Influenza Strain
The Type Influenza Strain template workflow is designed for typing targeted sequencing Influenza virus samples. It combines the Type with Consensus Refinement tool with a trimming step to determine the type and subtype of the Influenza virus. The workflow outputs a consensus sequence list, a list of the closest matching reference sequences, and annotation tracks (Genes and CDS) that are combined into a track list for easier visualization. Additionally, the workflow includes a Low Frequency Variant Detection step to detect potential mixed-infection variants, which can also be inspected in the same track list, both in nucleotide and amino acid formats.
Preliminary steps to run the Type a Known Species workflow
Before starting the workflow, download the Influenza Segment References data set using the Reference Data Manager.
How to run the Type Influenza Strain workflow
To run the workflow, go to:
Workflows | Template Workflows (
) | Microbial Workflows (
) | Typing and Epidemiology (
) | Type Influenza Strain (
)
- Specify the sample(s) or folder(s) of samples you would like to type and click Next.
- Click Next to use the automatically selected Influenza Segment References data set.
- Define batch units. For details, see Running workflows in batch mode.
- Check that batching is as intended.
- If your reads contain adapters, add an appropriate Trim adapter list. Click Next.
- Choose values for the parameters used for mixed infection variant detection (see Low Frequency Variant Detection).
- In the Create Sample Report step, various summary items have been set. These are guidelines to help evaluate the quality of the results (see Create Sample Report).
- In the Result handling window, pressing the button Preview All Parameters allows you to preview - but not change - all parameters. Choose to save the results (we recommend creating a new folder for it) and click Finish.
Outputs from the Type Influenza Strain workflow
The workflow produces the following outputs:
- QC & Reports. Folder containing the individual reports generated during the analysis.
- All reports from the sample report are found here in their full length.
- Sequences. Folder containing consensus sequence list and list of best-matching reference sequences.
- Tracks. Folder containing various tracks.
- Consensus sequence, Gene and CDS tracks based on the best-matching references.
- Read mapping. Reads track of the sample reads mapping to the consensus sequence.
- Candidate mixed infection variant. Variant track containing potential mixed infection variants.
- Candidate amino acid changes. Track to see amino acids and changes in coding sequences due to potential mixed infections.
- Consensus Genome Browser. A track list containing the consensus sequences, the annotation tracks, variant tracks and the read mappings. Individual tracks are located in the Tracks folder.
- Influenza Typing Report. Sample report containing results of the analysis. The sample report is curated to contain the most important information for analysis interpretation, but all full reports can be found in the QC & Reports folder.