mashtree
Tags: phylogeny tree mash distance comparison run-scope
Create phylogenetic trees using Mash distances.
This subworkflow uses Mashtree to rapidly compare whole genome sequence files and generate phylogenetic trees. It creates Mash sketches of input genomes, calculates pairwise distances, and constructs a tree based on the distance matrix.
Take
assemblies: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
fna | Pre-gathered assembled contigs in FASTA format (multiple genomes) |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
No sample-scope outputs.
run_outputs
| Output | Description |
|---|---|
nwk | Phylogenetic tree in Newick format |
tsv | Pairwise distance matrix |
sketches | Individual Mash sketch files |
Module Composition
This subworkflow calls the following modules:
- mashtree - Rapid alignment-free phylogenomic tree construction.
Used By
This subworkflow is used by the following workflows:
- mashtree - Rapid phylogenetic tree construction using Mash distances.
Citations
If you use this in your analysis, please cite the following.
-
Bactopia
Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020) -
Mashtree
Katz LS, Griswold T, Morrison S, Caravas J, Zhang S, den Bakker HC, Deng X, Carleton HA Mashtree: a rapid comparison of whole genome sequence files. Journal of Open Source Software, 4(44), 1762 (2019)