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 \ 
  --include includes.txt

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 (in GB) that can be requested for any single job. Type: `integer`, Default: `32`
`--max_time`	Maximum amount of time (in minutes) that can be requested for any single job. Type: `integer`, Default: `120`
`--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¶