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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​

FileDescription
*.kraken2.report.txtKraken2 classification report
*.bracken.report.txtBracken abundance estimates
*.krona.htmlKrona interactive visualization

Summary Reports​

FileDescription
bracken-summary.tsvSummary of classification results across all samples
bracken-matrix.tsvAbundance 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.

ExtensionDescription
.beginAn empty file used to designate the process started
.errContains STDERR outputs from the process
.logContains both STDERR and STDOUT outputs from the process
.outContains STDOUT outputs from the process
.runThe script Nextflow uses to stage/unstage files and queue processes based on given profile
.shThe script executed by bash for the process
.traceThe Nextflow trace report for the process
versions.ymlA 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.

FilenameDescription
bracken-dag.dotThe Nextflow DAG visualization
bracken-report.htmlThe Nextflow Execution Report
bracken-timeline.htmlThe Nextflow Timeline Report
bracken-trace.txtThe Nextflow Trace report

Parameters​

Required Parameters​

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

ParameterTypeDefaultDescription
--bactopiastringThe path to bactopia results to use as inputs

Kraken2 and Bracken Parameters​

ParameterTypeDefaultDescription
--kraken2_dbstringThe a single tarball or path to a Kraken2 formatted database
--kraken2_quick_modebooleanfalseQuick operation (use first hit or hits)
--kraken2_confidencenumber0.0Confidence score threshold between 0 and 1
--kraken2_minimum_base_qualityinteger0Minimum base quality used in classification
--kraken2_use_mpa_stylebooleanfalseFormat report output like Kraken 1's kraken-mpa-report
--kraken2_report_zero_countsbooleanfalseReport counts for ALL taxa, even if counts are zero
--kraken2_report_minimizer_databooleanfalseInclude minimizer and distinct minimizer count information in report
--kraken2_use_namesbooleanfalsePrint scientific names instead of just taxids
--kraken2_memory_mappingbooleanfalseAvoid loading database into RAM
--kraken2_minimum_hit_groupsinteger2Minimum number of hit groups needed to make a call
--kraken2_keep_filtered_readsbooleanfalseKeep the classified and unclassified FASTQs produced by Kraken2
--kraken2_keep_raw_outputbooleanfalseKeep the STDOUT file produced from Kraken2
--bracken_read_lengthinteger0Read length to get all classifications for (0 = determine at runtime)
--bracken_levelstringSLevel to estimate abundance at
--bracken_thresholdinteger0Reads required PRIOR to abundance estimation to perform re-estimation
--bracken_max_secondary_percentnumber0.01The maximum percent abundance for the secondary species, if exceeded, sample will remain unclassified
--bracken_skip_kronabooleanfalseSkip the creation of a Krona report

csvtk concat Parameters​

ParameterTypeDefaultDescription
--csvtk_concat_optsstringExtra csvtk concat options in quotes
Filtering Parameters

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

ParameterTypeDefaultDescription
--includestringA text file containing sample names (one per line) to include from the analysis
--excludestringA text file containing sample names (one per line) to exclude from the analysis
Optional Parameters

These optional parameters can be useful in certain settings.

ParameterTypeDefaultDescription
--outdirstringbactopiaBase directory to write results to
--skip_compressionbooleanfalseOutput files will not be compressed
--datasetsstringThe path to cache datasets to
--keep_all_filesbooleanfalseKeeps all analysis files created
Max Job Request Parameters

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

ParameterTypeDefaultDescription
--max_retryinteger3Maximum times to retry a process before allowing it to fail.
--max_cpusinteger4Maximum number of CPUs that can be requested for any single job.
--max_memorystring128.GBMaximum amount of memory that can be requested for any single job.
--max_timestring240.hMaximum amount of time that can be requested for any single job.
--max_downloadsinteger3Maximum number of samples to download at a time
Nextflow Configuration Parameters

Parameters to fine-tune your Nextflow setup.

ParameterTypeDefaultDescription
--nfconfigstringA Nextflow compatible config file for custom profiles, loaded last and will overwrite existing variables if set.
--publish_dir_modestringcopyMethod used to save pipeline results to output directory. (choices: symlink, rellink, link, copy, copyNoFollow, move)
--infodirstring${params.outdir}/pipeline_infoDirectory to keep pipeline Nextflow logs and reports.
--forcebooleanfalseNextflow will overwrite existing output files.
--cleanup_workdirbooleanfalseAfter 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.

ParameterTypeDefaultDescription
--custom_config_versionstringmasterGit commit id for Institutional configs.
--custom_config_basestringhttps://raw.githubusercontent.com/nf-core/configs/masterBase directory for Institutional configs.
--config_profile_namestringInstitutional config name.
--config_profile_descriptionstringInstitutional config description.
--config_profile_contactstringInstitutional config contact information.
--config_profile_urlstringInstitutional config URL link.
Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

ParameterTypeDefaultDescription
--condadirstringDirectory to Nextflow should use for Conda environments
--registrystringquay.ioRegistry to pull Docker containers from.
--datasets_cachestring<HOME>/.bactopia/datasetsDirectory where downloaded datasets should be stored.
--singularity_cachestringDirectory where remote Singularity images are stored.
--singularity_pull_docker_containerbooleanInstead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
--force_rebuildbooleanfalseForce overwrite of existing pre-built environments.
--queuestringgeneral,high-memoryComma-separated name of the queue(s) to be used by a job scheduler (e.g. AWS Batch or SLURM)
--cluster_optsstringAdditional options to pass to the executor. (e.g. SLURM: '--account=my_acct_name'
--container_optsstringAdditional options to pass to Apptainer, Docker, or Singularity. (e.g. Singularity: '-D pwd'
--disable_scratchbooleanfalseAll intermediate files created on worker nodes of will be transferred to the head node.
Helpful Parameters

Uncommonly used parameters that might be useful.

ParameterTypeDefaultDescription
--monochrome_logsbooleanDo not use coloured log outputs.
--nfdirbooleanPrint directory Nextflow has pulled Bactopia to
--sleep_timeinteger5The amount of time (seconds) Nextflow will wait after setting up datasets before execution.
--validate_paramsbooleantrueBoolean whether to validate parameters against the schema at runtime
--helpbooleanDisplay help text.
--wfstringbactopiaSpecify which workflow or Bactopia Tool to execute
--list_wfsbooleanList the available workflows and Bactopia Tools to use with '--wf'
--show_hidden_paramsbooleanShow all params when using --help
--help_allbooleanAn alias for --help --show_hidden_params
--versionbooleanDisplay 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.

Source​

View source on GitHub