Analyses: !Growth

Growth section

!Growth adds a section displaying the exact pangenome growth to the graph. Additionally, this section can show curves for the core and shell pangenome using coverage and quorum.

The pangenome growth describes how many features (nodes, edges, ...) one would expect on average if the graph was built from 1...n haplotypes.

In report.yaml

- !Growth
  coverage: 1,1,2
  quorum: 0,0.9,0

coverage specifies how often a feature needs to appear in the paths to be counted. This can for example be used to remove nodes of spurious evidence (e.g. due to errors in the sequencing process). coverage is applied during the preprocessing. quorum defines the ratio of paths that a feature appears in to be included in this specific bar of the output plot. This is applied during the growth calculation. Setting the quorum to 1 means that only features that are in every path of the current bar are counted, so it signifies the core genome. Setting to 0 is the whole pangenome growth, and values in between can be used for the shell pangenome.

coverage and quorum can be given as lists separated by commas. They are then treated as pairs, so the lists need to have the same lengths.