tbprofiler

Tags: mycobacterium-tuberculosis resistance lineage typing tb bactopia-tool

Detection of antimicrobial resistance and lineage typing of Mycobacterium tuberculosis.

This Bactopia Tool uses TBProfiler to profile Mycobacterium tuberculosis genomes for resistance mutations and strain typing. The workflow processes sequencing reads to identify resistance-conferring variants and determine the lineage of each TB isolate.

Usage

Bactopia CLI:

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

Nextflow:

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

Outputs

Expected Output Files

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── tbprofiler-<TIMESTAMP>
│           ├── <SAMPLE_NAME>.csv
│           ├── <SAMPLE_NAME>.results.json.gz
│           ├── <SAMPLE_NAME>.txt
│           ├── logs
│           │   ├── nf.command.{begin,err,log,out,run,sh,trace}
│           │   └── versions.yml
│           └── supplemental
│               ├── <SAMPLE_NAME>.bam
│               ├── <SAMPLE_NAME>.bam.bai
│               └── <SAMPLE_NAME>.targets.vcf.gz
└── bactopia-runs
    └── tbprofiler-<TIMESTAMP>
        ├── merged-results
        │   ├── logs
        │   │   └── tbprofiler-collate
        │   │       ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   ├── tbprofiler.csv
        │   ├── tbprofiler.variants.csv
        │   └── tbprofiler.variants.txt
        └── nf-reports
            ├── tbprofiler-dag.dot
            ├── tbprofiler-report.html
            └── tbprofiler-timeline.html

Per-Sample Results

File	Description
*.results.txt	Text file containing TBProfiler resistance and strain typing results
*.results.json	JSON file containing detailed TBProfiler analysis results
*.results.csv	CSV file containing TBProfiler results in tabular format
bam/*.bam	BAM file with read alignment details against reference genomes
vcf/*.targets.csq.vcf.gz	VCF file with variant annotations and functional consequences

Merged Results

File	Description
tbprofiler.tsv	Merged TSV file containing TBProfiler 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
tbprofiler-dag.dot	The Nextflow DAG visualization
tbprofiler-report.html	The Nextflow Execution Report
tbprofiler-timeline.html	The Nextflow Timeline Report
tbprofiler-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

TB-Profiler Profile Parameters

Parameter	Type	Default	Description
--tbprofiler_call_whole_genome	boolean	false	Call whole genome
--tbprofiler_mapper	string	bwa	Mapping tool to use. If you are using nanopore data it will default to minimap2 (choices: bwa, minimap2, bowtie2, bwa-mem2)
--tbprofiler_caller	string	freebayes	Variant calling tool to use (choices: bcftools, gatk, freebayes)
--tbprofiler_opts	string		Extra options in quotes for TBProfiler

TB-Profiler Collate Parameters

Parameter	Type	Default	Description
--tbprofiler_itol	boolean	false	Generate itol config files
--tbprofiler_full	boolean	false	Output mutations in main result file
--tbprofiler_all_variants	boolean	false	Output all variants in variant matrix
--tbprofiler_mark_missing	boolean	false	An asterisk will be used to mark predictions which are affected by missing data at a drug resistance position

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:

• tbprofiler - Profiling tool for Mycobacterium tuberculosis to detect resistance and strain type.

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)

• TBProfiler
  Phelan JE, O'Sullivan DM, Machado D, Ramos J, Oppong YEA, Campino S, O'Grady J, McNerney R, Hibberd ML, Viveiros M, Huggett JF, Clark TG Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. Genome Med 11, 41 (2019)

Source

View source on GitHub