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Workflows available

Assembly_Fetch

Augur

Concatenate_Column_Content

Core_Gene_SNP

Freyja Wastewater Analysis

Kraken2

kSNP3

Lyve_SET

MashTree_FASTA

Mercury_Prep_N_Batch

Pangolin Update

Rasusa

Snippy_Streamline

Snippy_Tree

Snippy_Variants

SRA_Fetch

Terra_2_GISAID

Terra_2_NCBI

TheiaCoV Genomic Characterization

TheiaEuk

TheiaMeta

TheiaProk Workflow Series

TheiaValidate

Usher_PHB

VADR_Update

Zip_Column_Content

Overview

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 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

Inputs

Tasks

Outputs

References

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