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Bactopia Tool - bracken

The bracken module uses Bracken to estimate taxonomic abundance of samples. This Bactopia Tool will also run Kraken2, automatically and generate Krona charts for both Bracken and Kraken2.

Example Usage

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

Output Overview

Below is the default output structure for the bracken tool. Where possible the file descriptions below were modified from a tools description.

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── bracken
│           ├── <SAMPLE_NAME>.bracken.abundances.txt
│           ├── <SAMPLE_NAME>.bracken.adjusted.abundances.txt
│           ├── <SAMPLE_NAME>.bracken.krona.html
│           ├── <SAMPLE_NAME>.bracken.report.txt
│           ├── <SAMPLE_NAME>.bracken.tsv
│           ├── <SAMPLE_NAME>.classified_{1,2}.fastq.gz
│           ├── <SAMPLE_NAME>.kraken2.krona.html
│           ├── <SAMPLE_NAME>.kraken2.output.txt
│           ├── <SAMPLE_NAME>.kraken2.report.txt
│           ├── <SAMPLE_NAME>.unclassified_{1,2}.fastq.gz
│           └── logs
│               ├── nf-bracken.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── bracken-<TIMESTAMP>
        └── nf-reports
            ├── bracken-dag.dot
            ├── bracken-report.html
            ├── bracken-timeline.html
            └── bracken-trace.txt

Results

Bracken & Kraken2

Below is a description of the per-sample results from Bracken and Kraken2.

Filename Description
<SAMPLE_NAME>.bracken.abundances.txt Bracken abundance estimates for each taxon.
<SAMPLE_NAME>.bracken.adjusted.abundances.txt Bracken abundance estimates for each taxon adjusted for inclusion of unclassified reads
<SAMPLE_NAME>.bracken.krona.html Krona chart of Bracken abundance estimates
<SAMPLE_NAME>.bracken.report.txt Bracken report containing stats about classified and not classified reads See Bracken - Output Formats
<SAMPLE_NAME>.classified_{1 2}.fastq.gz
<SAMPLE_NAME>.kraken2.krona.html Krona chart of Kraken2 abundance estimates
<SAMPLE_NAME>.kraken2.output.txt Kraken2 output file containing the taxonomic classification of each read
<SAMPLE_NAME>.kraken2.report.txt Kraken2 report containing stats about classified and not classified reads See Kraken2 - Output Formats for more details
<SAMPLE_NAME>.unclassified_{1,2}.fastq.gz Reads not classified to belong to any of the taxa on the Kraken2 database.

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 visualisation
bracken-report.html The Nextflow Execution Report
bracken-timeline.html The Nextflow Timeline Report
bracken-trace.txt The Nextflow Trace report

Program Versions

At the end of each run, each of the versions.yml files are merged into the files below.

Filename Description
software_versions.yml A complete list of programs and versions used by each process
software_versions_mqc.yml A complete list of programs and versions formatted for MultiQC

Parameters

Required Parameters

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

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

Filtering Parameters

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

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

Kraken2 and Bracken Parameters

Parameter Description
--kraken2_db The a single tarball or path to a Kraken2 formatted database
Type: string
--kraken2_quick_mode Quick operation (use first hit or hits)
Type: boolean
--kraken2_confidence Confidence score threshold between 0 and 1
Type: number
--kraken2_minimum_base_quality Minimum base quality used in classification
Type: integer
--kraken2_use_mpa_style Format report output like Kraken 1's kraken-mpa-report
Type: boolean
--kraken2_report_zero_counts Report counts for ALL taxa, even if counts are zero
Type: boolean
--kraken2_report_minimizer_data Include minimizer and distinct minimizer count information in report
Type: boolean
--kraken2_use_names Print scientific names instead of just taxids
Type: boolean
--kraken2_memory_mapping Avoid loading database into RAM
Type: boolean
--kraken2_minimum_hit_groups Minimum number of hit groups needed to make a call
Type: integer, Default: 2
--kraken2_remove_filtered_reads Discard the classified and unclassified FASTQs prduced by Kraken2
Type: boolean
--kraken2_keep_raw_output Keep the STDOUT file produced from Kraken2
Type: boolean
--bracken_read_length Read length to get all classifications for (0 = determine at runtime)
Type: integer
--bracken_level Level to estimate abundance at
Type: string, Default: S
--bracken_threshold Reads required PRIOR to abundance estimation to perform re-estimation
Type: integer
--skip_krona Skip the creation of a Krona report
Type: boolean

Optional Parameters

These optional parameters can be useful in certain settings.

Parameter Description
--outdir Base directory to write results to
Type: string, Default: bactopia
--skip_compression Ouput files will not be compressed
Type: boolean
--datasets The path to cache datasets to
Type: string
--keep_all_files Keeps all analysis files created
Type: boolean

Max Job Request Parameters

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

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

Nextflow Configuration Parameters

Parameters to fine-tune your Nextflow setup.

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

Institutional config options

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

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

Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

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

Helpful Parameters

Uncommonly used parameters that might be useful.

Parameter Description
--monochrome_logs Do not use coloured log outputs.
Type: boolean
--nfdir Print directory Nextflow has pulled Bactopia to
Type: boolean
--sleep_time The amount of time (seconds) Nextflow will wait after setting up datasets before execution.
Type: integer, Default: 5
--validate_params Boolean whether to validate parameters against the schema at runtime
Type: boolean, Default: True
--help Display help text.
Type: boolean
--wf Specify which workflow or Bactopia Tool to execute
Type: string, Default: bactopia
--list_wfs List the available workflows and Bactopia Tools to use with '--wf'
Type: boolean
--show_hidden_params Show all params when using --help
Type: boolean
--help_all An alias for --help --show_hidden_params
Type: boolean
--version Display version text.
Type: boolean

Citations

If you use Bactopia and bracken in your analysis, please cite the following.