Type with Consensus Refinement parameters
To run the tool, go to:
Tools | Microbial Genomics Module (
) | Typing and Epidemiology (
) | Type with Consensus Refinement (
)
In the first dialog, select the reads for analysis, and click on Next.
Click Next to select a reference database. The reference database is a sequence list in which each sequence must be annotated with a Segment attribute. The tool uses the Segment information to define which sequences will be considered together when evaluating which of them suits better the input data. The sequences in the reference may also be annotated with a Type attribute (e.g. A and B) and a Subtype attribute (e.g. H1 and H5). Sequence lists can be updated manually in the Table View or using a table file with Update Sequence Attributes in Lists.
A ready-to-use reference data set for typing Influenza A, B, C and D is available through the Reference Data Manager.
In the Mapping options dialog, specify settings for the read mapping (figure 8.10). The options are identical to those of the Map Reads to Reference tool, except for the "Non-specific match handling".
Figure 8.10: Select mapping options.
The Filters dialog holds the following options (figure 8.11):
- Minimum count. Minimum number of mapped reads required for a reference to be reported.
- Minimum relative abundance. Minimum relative abundance compared to most abundant reference required for a reference to be reported.
- Minimum fraction of reference covered. Minimum fraction of the reference sequence to be covered by at least one read for a reference to be reported.
- Minimum average coverage. Minimum average coverage for a reference to be reported, whereas average coverage is the number of nucleotides mapped to a reference divided by the reference length.
- Maximum number of references to report. The maximum number of references to report. References are ranked according to the number of mapped reads.
Figure 8.11: Choose your output option before saving your results.
Note that all filters apply per sequence, except for the Minimum relative abundance and Maximum number of references to report filters which consider all sequences with the same Segment and Type (if present). In the Minimum relative abundance case, if four references for Influenza A segment 3 are available for example, the filter considers the relative abundance among these four sequences and ignores the abundance in the rest of the references. In the Maximum number of references to report case, if the value is set to three, for a virus with eight segments such as Influenza, up to 24 segments may be reported (up to three per segment).