Map to Specified Reference

Once analysis has been performed using the Type a Known Species or the Type among Multiple Species workflow, the best matching reference is listed in the Result Metadata table (figure 11.1, see column Best match).

Image rmt_first_filter_wf
Figure 11.1: Best match references are listed for each row in the Result Metadata Table.

If all your samples share the same common reference, you can proceed to additional analyses without delay.

However there are cases where your samples have different Best match reference for a particular MLST scheme. And because creating a SNP Tree require a single common reference, you will need to identify the best matching common reference for all your samples using a K-mer Tree, as well as subsequently re-map your samples to this common reference.

If you already know the common reference for the sample you want to use to create a SNP tree, you can directly specify that reference in the re-map workflow. Otherwise, finding a common reference is described in more details in section 12.2.

In short, to identify a common reference across multiple clades within the Result Metadata Table:

The common reference, chosen as sharing the closest common ancestor with the clade of isolates under study in the k-mer tree, is subsequently used as a reference for the Map to Specified Reference workflow (figure 11.2) that will perform a re-mapping of the reads followed by variant calling.

Image remap_small
Figure 11.2: Overview of the template Map to Specified Reference workflow.