Taxonomy curation

Goals

1. Modify existing taxonomic assignments of genomes based on a phylogenetic tree.
2. Evaluate degree of consistency between existing taxonomic units and the tree.
3. Annotate tips and internal nodes of the tree with taxonomic lineages.

Summary

We use tax2tree (McDonald et al., 2012), which was originally developed by our team, and was used to curate multiple reference databases such as Greengenes and GTDB.

Naming rule

This analysis does NOT create new taxonomic units.

If a taxonomic unit is strongly polyphyletic (i.e., members of this unit form multiple separate clades in a tree), tax2tree will append a numeric suffix to it for each clade, sorted by taxon number from high to low (e.g., Firmicutes_1, Firmicutes_2…).

Code

We provide the whole pipeline in tax2tree_curation.ipynb. It explains how to run tax2tree, and performs subsequent manipulations to generate a range of useful files, including per-rank tables and lineage strings at tips and internal nodes.