bracken

Tags: metagenomics classification taxonomy abundance kraken2 bracken krona sample-scope

Taxonomic classification and abundance estimation.

Uses Kraken2 to classify reads against a taxonomic database, followed by Bracken (Bayesian Reestimation of Abundance with KrakEN) to estimate relative abundances at a specific taxonomic level. It also generates an interactive Krona plot for visualization.

Uses explicit positional record fields for reads:

• Input: record(meta, r1, r2, se, lr) where each read slot is Path?

Database Required

Requires a compatible Kraken2/Bracken database (tarball).

Inputs

record (
    meta: Record,
    r1: Path?,
    r2: Path?,
    se: Path?,
    lr: Path?
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
r1	Path?	Illumina R1 reads (paired-end)
r2	Path?	Illumina R2 reads (paired-end)
se	Path?	Single-end Illumina reads
lr	Path?	Long reads (ONT/PacBio) - not typically used

db: Path

Name	Type	Description
db	Path	A compressed tarball containing the Kraken2/Bracken database

Outputs

record (
    meta: Record,
    tsv: Path,
    special_meta: Record,
    classified: Set<Path?>,
    unclassified: Set<Path?>,
    kraken2_report: Path,
    kraken2_output: Path?,
    bracken_report: Path,
    krona: Set<Path?>,
    abundances: Path,
    classification: Path,
    adjusted_abundances: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Tab-delimited summary of Bracken primary and secondary species abundances
special_meta	Record	A simplified metadata record for internal use
classified	Set<Path?>	Reads classified to belong to any of the taxa on the Kraken2 database
unclassified	Set<Path?>	Reads not classified to belong to any of the taxa on the Kraken2 database
kraken2_report	Path	Kraken2 report containing stats about classified and not classified reads
kraken2_output	Path?	Kraken2 output file containing the taxonomic classification of each read
bracken_report	Path	Bracken report containing stats about classified and not classified reads
krona	Set<Path?>	Interactive Krona HTML visualization
abundances	Path	Bracken abundance estimates for each taxon
classification	Path	Bracken per-read classification details
adjusted_abundances	Path	Bracken abundance estimates adjusted for unclassified reads
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

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

Used By

Subworkflows

• bracken - Estimate species abundance from metagenomic reads.

Workflows

• bracken - Estimate taxonomic abundance of metagenomic samples.

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

Version

BRACKEN:
    - bactopia-teton: 1.1.3