MashTree

What does it do?

MashTree will take a list of SEQIDs, and then create a phylogenetic tree using Mash distances. See mashtree github and the mashtree docs for more information. (The mashtree docs explains how mash is used to create the phylogeny).

If you use mashtree, please remember to cite Katz et al., 2019, Ondov et al., 2016 and Ondov et al., 2019

How do I use it?

Subject

In the Subject field, put mashtree. Spelling counts, but case sensitivity doesn't.

Description

Required Components

The first line of the description should be the analysis you would like to run (e.g. analysis=custom).

  • The following options are currently supported:
    • custom - compare only the SEQIDs listed in the description
    • enterobacterales - compare the listed SEQIDs to a set of reference sequences for species from the order Enterobacterales
    • listeriaceae - compare the listed SEQIDs to a set of reference sequences for species from the family Listeriaceae

You must also include a list of SEQIDs one per line.

Optional Components

  • genomesize:

    • default is 5000000
    • If you want to use a genome size estimate, add a line to your description:
      • genomesize=3000000

  • mindepth - if mindepth is zero, then it will be chosen in a smart but slower method to discard lower-abundance kmers.

    • default is 5
    • If you want to use a minimum depth, add a line to your description:
      • mindepth=10

  • kmerlength - Mash kmer size "larger k-mers will provide more specificity while smaller k-mers will provide more sensitivity. (Larger genomes will also require larger k-mers to avoid k-mers that are shared by chance)."

    • default is 21
    • If you want to change the k-mer size, add a line to your description:
      • kmerlength=30

  • sketch-size - Mash sketch size "corresponds to the number of (non-redundant) min-hashes that are kept. Larger sketches will better represent the sequence, but at the cost of larger sketch files and longer comparison times."

    • default is 10000
    • If you want to change the mash sketch-size, add a line to your description:
      • sketch-size=1000

Example

For an example MashTree, see issue 26206.

Interpreting Results

Upon completion, you'll be given a treefile.

How long does it take?

This depends largely on the number of strains you want to use to create the tree. It can often be as quick as a few minutes.

What can go wrong?

A few things can go wrong with this process:

1) Requested SEQIDs are not available. If we can't find some of the SEQIDs that you request, you will get a warning message informing you of it.

Version

Version 0.35.4 is currently available at the OLC. (as of 2024-07-4)