Snippy_Tree is a workflow for generating high-quality bacterial phylogenies. It produces a phylogenetic tree and pairwise SNP-distance matrix, with the option to summarize additional metadata to visualize with the tree.

The tree produced by Snippy_Tree will always be a maximum-likelihood phylogeny using a reference-based alignment. There are key options for whether to:

Generate a core-genome or whole-genome phylogeny (core_genome)
Mask specified regions of the genome with a bed file (e.g. known repetitive regions for TB) (bed_file)
Mask recombination (use_gubbins)
Decide which nucleotide substitution model to use

Workflows available

Overview

Inputs

Tasks

Outputs

References