kraken2
Tags: metagenomics taxonomic-classification kraken2 k-mer sample-scope
Classify metagenomic reads using Kraken2.
This subworkflow performs taxonomic classification of metagenomic reads using Kraken2, a fast taxonomic classification system. It assigns taxonomic labels to sequencing reads based on k-mer matching against a reference database.
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 |
|---|---|
kraken2_report | Standard Kraken2 report containing taxonomic abundance counts |
scrub_report | Summary report of reads removed during host scrubbing (optional) |
special_meta | A simplified metadata record for internal use |
classified | Reads assigned to a taxon in the database (FASTQ) |
unclassified | Reads NOT assigned to any taxon (FASTQ) |
run_outputs
No run-scope outputs.
Module Composition
This subworkflow calls the following modules:
- kraken2 - Taxonomic classification and host filtering of sequence reads.
Used By
This subworkflow is used by the following workflows:
- kraken2 - Taxonomic classification of metagenomic sequence reads.
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)