gtdb

Tags: taxonomy classification marker-genes phylogeny gtdb bactopia-tool

Identify marker genes and assign taxonomic classifications using GTDB.

This Bactopia Tool uses GTDB-Tk's classify workflow to assign taxonomic classifications to samples using the Genome Taxonomy Database.

Usage

Bactopia CLI:

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

Nextflow:

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

Outputs

Expected Output Files

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── gtdb-<TIMESTAMP>
│           ├── <SAMPLE_NAME>.bac120.summary.tsv
│           ├── logs
│           │   ├── gtdbtk.log
│           │   ├── gtdbtk.warnings.log
│           │   ├── nf.command.{begin,err,log,out,run,sh,trace}
│           │   └── versions.yml
│           └── supplemental
│               ├── classify
│               │   └── ani_screen
│               │       └── <SAMPLE_NAME>.bac120.ani_summary.tsv
│               └── gtdbtk.json
└── bactopia-runs
    └── gtdb-<TIMESTAMP>
        ├── merged-results
        │   ├── gtdb.tsv
        │   └── logs
        │       └── gtdb-concat
        │           ├── nf.command.{begin,err,log,out,run,sh,trace}
        │           └── versions.yml
        └── nf-reports
            ├── gtdb-dag.dot
            ├── gtdb-report.html
            └── gtdb-timeline.html

Taxonomic Classification

File	Description
*.summary.tsv	Taxonomic classification summary
*.gtdbtk.tsv	Detailed GTDB-Tk results

Merged Results

File	Description
gtdb.tsv	Merged TSV file containing GTDB results from all samples

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
gtdb-dag.dot	The Nextflow DAG visualization
gtdb-report.html	The Nextflow Execution Report
gtdb-timeline.html	The Nextflow Timeline Report
gtdb-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

GTDB-Tk Setup Database Parameters

Parameter	Type	Default	Description
--gtdb	string		Tarball or path of a GTDB database. If a database is not found, you must use '--download_gtdb'
--download_gtdb	boolean	false	Download the latest GTDB database, even it exists
--gtdb_save_as_tarball	boolean	false	Download the latest GTDB database, and save it in a single tarball

GTDB Classify Parameters

Parameter	Type	Default	Description
--gtdb_min_af	number	0.65	Minimum alignment fraction to consider closest genome
--gtdb_min_perc_aa	integer	10	Filter genomes with an insufficient percentage of AA in the MSA
--force_gtdb	boolean	false	Continue processing if an error occurs on a single genome

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:

• gtdb - Taxonomic classification with the Genome Taxonomy 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)

• Genome Taxonomy Database
  Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil P-A, Hugenholtz P GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy Nucleic Acids Research gkab776 (2021)

Source

View source on GitHub