mashtree

Tags: phylogeny tree mash distance comparative-genomics bactopia-tool

Rapid phylogenetic tree construction using Mash distances.

This Bactopia Tool uses Mashtree to create a phylogenetic tree of samples using Mash distances. It can include reference genomes from RefSeq by downloading them with NCBI genome download.

Usage

Bactopia CLI:

bactopia --wf mashtree \
  --bactopia /path/to/your/bactopia/results

Nextflow:

nextflow run bactopia/bactopia/workflows/bactopia-tools/mashtree/main.nf \
  --bactopia /path/to/your/bactopia/results

Outputs

Expected Output Files

<BACTOPIA_DIR>
└── <SAMPLE_NAME>
    └── mashtree-<TIMESTAMP>
        ├── logs
        │   ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   └── versions.yml
        ├── mashtree.dnd
        ├── mashtree.tsv
        └── nf-reports
            ├── mashtree-dag.dot
            ├── mashtree-report.html
            └── mashtree-timeline.html

Phylogenetic Analysis

File	Description
mashtree.dnd	Newick format tree file
mashtree.tsv	Tab-delimited distance matrix

Merged Results

File	Description
mashtree-summary.tsv	Merged summary of all Mashtree results

Audit Trail

Below are files that can assist you in understanding which parameters and program versions were used.

Logs

Each process that is executed will have a folder named logs. In this folder are helpful files for you to review if the need ever arises.

Extension	Description
.begin	An empty file used to designate the process started
.err	Contains STDERR outputs from the process
.log	Contains both STDERR and STDOUT outputs from the process
.out	Contains STDOUT outputs from the process
.run	The script Nextflow uses to stage/unstage files and queue processes based on given profile
.sh	The script executed by bash for the process
.trace	The Nextflow trace report for the process
versions.yml	A YAML formatted file with program versions

Nextflow Reports

These Nextflow reports provide great a great summary of your run. These can be used to optimize resource usage and estimate expected costs if using cloud platforms.

Filename	Description
mashtree-dag.dot	The Nextflow DAG visualization
mashtree-report.html	The Nextflow Execution Report
mashtree-timeline.html	The Nextflow Timeline Report
mashtree-trace.txt	The Nextflow Trace report

Parameters

Required Parameters

Define where the pipeline should find input data and save output data.

Parameter	Type	Default	Description
--bactopia	string		The path to bactopia results to use as inputs

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

NCBI Genome Download Parameters

Parameter	Type	Default	Description
--species	string		Name of the species to download assemblies
--accession	string		An NCBI Assembly accession to be downloaded
--accessions	string		An file of NCBI Assembly accessions (one per line) to be downloaded
--format	string	fasta	Comma separated list of formats to download
--limit	string		Limit the number of assemblies to download
--keep_downloads	boolean	false	Save downloaded files into the bactopia-runs folder

Filtering Parameters

Use these parameters to specify which samples to include or exclude.

Parameter	Type	Default	Description
--include	string		A text file containing sample names (one per line) to include from the analysis
--exclude	string		A text file containing sample names (one per line) to exclude from the analysis

Optional Parameters

These optional parameters can be useful in certain settings.

Parameter	Type	Default	Description
--outdir	string	bactopia	Base directory to write results to

Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

Parameter	Type	Default	Description
--datasets_cache	string	<HOME>/.bactopia/datasets	Directory where downloaded datasets should be stored.

Helpful Parameters

Uncommonly used parameters that might be useful.

Parameter	Type	Default	Description
--wf	string	bactopia	Specify which workflow or Bactopia Tool to execute
--list_wfs	boolean		List the available workflows and Bactopia Tools to use with '--wf'
--help_all	boolean		An alias for --help --show_hidden_params
--version	boolean		Display version text.

Composition

This workflow uses the following subworkflows:

• mashtree - Create phylogenetic trees using Mash distances.
• ncbigenomedownload - Download bacterial genomes from NCBI's RefSeq database.

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