bracken

Tags: metagenomics classification abundance kraken2 bracken krona bactopia-tool

Estimate taxonomic abundance of metagenomic samples.

This Bactopia Tool uses Bracken to estimate taxonomic abundance from Kraken2 results. It also runs Kraken2 for taxonomic classification and generates Krona interactive charts.

Usage

Bactopia CLI:

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

Nextflow:

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

Outputs

Expected Output Files

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── bracken-<TIMESTAMP>
│           ├── <SAMPLE_NAME>.bracken.abundances.txt
│           ├── <SAMPLE_NAME>.bracken.adjusted.abundances.txt
│           ├── <SAMPLE_NAME>.bracken.classification.txt
│           ├── <SAMPLE_NAME>.bracken.krona.html
│           ├── <SAMPLE_NAME>.bracken.report.txt
│           ├── <SAMPLE_NAME>.bracken.tsv
│           ├── <SAMPLE_NAME>.kraken2.krona.html
│           ├── <SAMPLE_NAME>.kraken2.report.txt
│           └── logs
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── bracken-<TIMESTAMP>
        ├── merged-results
        │   ├── bracken-adjusted.tsv
        │   ├── bracken-species-abundance.tsv
        │   └── logs
        │       ├── bracken-adjusted-concat
        │       │   ├── nf.command.{begin,err,log,out,run,sh,trace}
        │       │   └── versions.yml
        │       └── bracken-species-abundance-concat
        │           ├── nf.command.{begin,err,log,out,run,sh,trace}
        │           └── versions.yml
        └── nf-reports
            ├── bracken-dag.dot
            ├── bracken-report.html
            └── bracken-timeline.html

Classification Results

File	Description
*.kraken2.report.txt	Kraken2 classification report
*.bracken.report.txt	Bracken abundance estimates
*.krona.html	Krona interactive visualization

Summary Reports

File	Description
bracken-summary.tsv	Summary of classification results across all samples
bracken-matrix.tsv	Abundance matrix for downstream analysis

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

Kraken2 and Bracken Parameters

Parameter	Type	Default	Description
--kraken2_db	string		The a single tarball or path to a Kraken2 formatted database
--kraken2_confidence	number	0.0	Confidence score threshold between 0 and 1
--kraken2_use_mpa_style	boolean	false	Format report output like Kraken 1's kraken-mpa-report
--kraken2_report_zero_counts	boolean	false	Report counts for ALL taxa, even if counts are zero

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:

• bracken - Estimate species abundance from metagenomic reads.

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)

• Bracken
  Lu J, Breitwieser FP, Thielen P, and Salzberg SL Bracken: estimating species abundance in metagenomics data. PeerJ Computer Science, 3, e104. (2017)

• Kraken2
  Wood DE, Lu J, Langmead B Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. (2019)

• Krona
  Ondov BD, Bergman NH, and Phillippy AM Interactive metagenomic visualization in a Web browser. BMC Bioinformatics, 12, 385. (2011)

Source

View source on GitHub