3. Nomenclature
ReporTree cluster names follow a regular expression:
- cluster_N - for each genetic cluster (i.e. >= 2 samples) found at each threshold of the current analysis (e.g. cluster_1)
- singleton_N - for each sample that does not belong to a cluster at a given threshold of the current analysis (e.g. singleton_1)
To facilitate routine surveillance and cluster monitoring over time, the user can provide the 'partitions.tsv' from the previous run in the '--nomenclature-file' argument, and ReporTree will use this information to (re)name the clusters in the current run. Below, we show a summary of the behavior of the “Cluster Nomenclature System” in some of the most common situations in a routine surveillance scenario:
Details about these and other situations are presented in the following table:
Of note, to increase the flexibility of the nomenclature system, ReporTree also allows the users to change the regular expression for cluster nomenclature (i.e., starting with “cluster_” or “singleton_”) by other nomenclature of interest (e.g., other official codes for outbreaks, genogroups, etc.), which will be kept afterwards. If the cluster/singleton names do not follow ReporTree's regular expression, the rules mentioned in the above table will be applied, except for the particular situation in which the name a former singleton does not follow ReporTree's regular expression. In this case, if a sigleton named as 'mycode' integrates a cluster only with new samples, this new cluster will be named 'mycode'.