mashtree

Tags: phylogeny tree mash minhash alignment-free distance clustering neighbor-joining run-scope

Rapid alignment-free phylogenomic tree construction.

Uses Mashtree to create a phylogenetic tree from genome sequences (FASTA, FASTQ, or GenBank) using MinHash distances. It computes pairwise distances between all inputs and uses the Neighbor-Joining algorithm to cluster genomes, effectively creating a "distance-based" tree without full alignment.

Inputs

record (
    meta: Record,
    fna: Set<Path>
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Set<Path>	Assembled contigs in FASTA format

Outputs

record (
    meta: Record,
    nwk: Path,
    tsv: Path,
    sketches: Set<Path?>,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
nwk	Path	The final phylogenetic tree in Newick format (*.dnd)
tsv	Path	The pairwise distance matrix used to build the tree (*.tsv)
sketches	Set<Path?>	Directory containing the individual Mash sketches
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

Mashtree Parameters

Parameter	Type	Default	Description
--mashtree_sortorder	string	ABC	For neighbor-joining, the sort order can make a difference. (choices: ABC, random, input-order)
--mashtree_genomesize	integer	5000000	Genome size of the input samples
--mashtree_mindepth	integer	5	If mindepth is zero, then it will be chosen in a smart but slower method, to discard lower-abundance kmers.
--mashtree_kmerlength	integer	21	Hashes will be based on strings of this many nucleotides

Used By

Subworkflows

• mashtree - Create phylogenetic trees using Mash distances.

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)

Source

View source on GitHub

Version

MASHTREE:
    - mashtree: 1.4.6