bracken
Tags: metagenomics taxonomic-classification abundance-estimation kraken2 bracken sample-scope
Estimate species abundance from metagenomic reads.
This subworkflow performs taxonomic classification and abundance estimation using Kraken2 and Bracken. It processes metagenomic reads, classifies them against a reference database, and generates abundance estimates at different taxonomic levels with optional abundance correction.
Uses explicit positional record fields for reads:
- Input: record(meta, r1, r2, se, lr) where each read slot is Path?
Take
reads: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
r1 | Illumina R1 reads (paired-end) |
r2 | Illumina R2 reads (paired-end) |
se | Single-end Illumina reads |
lr | Long reads (ONT/PacBio) |
database: Path
| Name | Type | Description |
|---|---|---|
database | Path | Path to the Kraken2 database for taxonomic classification. |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
tsv | Tab-delimited summary of Bracken primary and secondary species abundances |
special_meta | A simplified metadata record for internal use |
classified | Reads classified to belong to any of the taxa on the Kraken2 database |
unclassified | Reads not classified to belong to any of the taxa on the Kraken2 database |
kraken2_report | Kraken2 report containing stats about classified and not classified reads |
kraken2_output | Kraken2 output file containing the taxonomic classification of each read |
bracken_report | Bracken report containing stats about classified and not classified reads |
krona | Interactive Krona HTML visualization |
abundances | Bracken abundance estimates for each taxon |
classification | Bracken per-read classification details |
adjusted_abundances | Bracken abundance estimates adjusted for unclassified reads |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- bracken - Taxonomic classification and abundance estimation.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following 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) -
Kraken2
Wood DE, Lu J, Langmead B Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. (2019) -
Bracken
Lu J, Breitwieser FP, Thielen P, and Salzberg SL Bracken: estimating species abundance in metagenomics data. PeerJ Computer Science, 3, e104. (2017)