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 NCBI by downloading them with genome-dl.

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_trunclength	integer	250	How many characters to keep in a filename
--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
--mashtree_sketchsize	integer	10000	Each sketch will have at most this many non-redundant min-hashes
--mashtree_save_sketches	boolean	false	Save sketches created during the process

genome-dl 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
--section	string	refseq	NCBI section to download
--assembly_level	string	complete	Comma separated list of assembly levels to download
--limit	integer	100	Limit the number of assemblies to download
--genomedl_allow_outdated	boolean	false	Download an explicitly requested outdated accession version instead of erroring

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
--skip_compression	boolean	false	Output files will not be compressed
--datasets	string	-	The path to cache datasets to
--keep_all_files	boolean	false	Keeps all analysis files created

Max Job Request Parameters

Set the top limit for requested resources for any single job.

Parameter	Type	Default	Description
--max_retry	integer	3	Maximum times to retry a process before allowing it to fail.
--max_cpus	integer	4	Maximum number of CPUs that can be requested for any single job.
--max_memory	string	128.GB	Maximum amount of memory that can be requested for any single job.
--max_time	string	240.h	Maximum amount of time that can be requested for any single job.
--max_downloads	integer	3	Maximum number of samples to download at a time

Nextflow Configuration Parameters

Parameters to fine-tune your Nextflow setup.

Parameter	Type	Default	Description
--nfconfig	string	-	A Nextflow compatible config file for custom profiles, loaded last and will overwrite existing variables if set.
--publish_dir_mode	string	copy	Method used to save pipeline results to output directory. (choices: symlink, rellink, link, copy, copyNoFollow, move)
--infodir	string	${params.outdir}/pipeline_info	Directory to keep pipeline Nextflow logs and reports.
--force	boolean	false	Nextflow will overwrite existing output files.
--cleanup_workdir	boolean	false	After Bactopia is successfully executed, the work directory will be deleted.

Institutional config options

Parameters used to describe centralized config profiles. These should not be edited.

Parameter	Type	Default	Description
--custom_config_version	string	master	Git commit id for Institutional configs.
--custom_config_base	string	https://raw.githubusercontent.com/nf-core/configs/master	Base directory for Institutional configs.
--config_profile_name	string	-	Institutional config name.
--config_profile_description	string	-	Institutional config description.
--config_profile_contact	string	-	Institutional config contact information.
--config_profile_url	string	-	Institutional config URL link.

Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

Parameter	Type	Default	Description
--condadir	string	-	Directory to Nextflow should use for Conda environments
--registry	string	quay.io	Registry to pull Docker containers from.
--datasets_cache	string	<HOME>/.bactopia/datasets	Directory where downloaded datasets should be stored.
--singularity_cache	string	-	Directory where remote Singularity images are stored.
--singularity_pull_docker_container	boolean	-	Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
--force_rebuild	boolean	false	Force overwrite of existing pre-built environments.
--queue	string	general,high-memory	Comma-separated name of the queue(s) to be used by a job scheduler (e.g. AWS Batch or SLURM)
--cluster_opts	string		Additional options to pass to the executor. (e.g. SLURM: '--account=my_acct_name'
--container_opts	string		Additional options to pass to Apptainer, Docker, or Singularity. (e.g. Singularity: '-D pwd'
--disable_scratch	boolean	false	All intermediate files created on worker nodes of will be transferred to the head node.

Helpful Parameters

Uncommonly used parameters that might be useful.

Parameter	Type	Default	Description
--monochrome_logs	boolean	-	Do not use coloured log outputs.
--nfdir	boolean	-	Print directory Nextflow has pulled Bactopia to
--sleep_time	integer	5	The amount of time (seconds) Nextflow will wait after setting up datasets before execution.
--help	boolean	-	Display help text.
--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'
--show_hidden_params	boolean	-	Show all params when using --help
--help_all	boolean	-	An alias for --help --show_hidden_params
--version	boolean	-	Display version text.

Composition

This workflow uses the following subworkflows:

• genomedl - Download genome assemblies from NCBI Datasets.
• mashtree - Create phylogenetic trees 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