kraken2

Tags: metagenomics taxonomy classification contamination scrubbing k-mer lca sample-scope

Taxonomic classification and host filtering of sequence reads.

Uses Kraken2 to assign taxonomic labels to short DNA reads by examining exact k-mer matches against a large reference database. It uses the Lowest Common Ancestor (LCA) algorithm to provide high-precision classification, making it ideal for metagenomics or removing host contamination (scrubbing).

Uses explicit positional record fields for reads:

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

Database Required

Requires a standard Kraken2 database (directory or tarball). Memory usage depends on database size (Standard ~50GB).

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 by Kraken2

db: Path

Name	Type	Description
db	Path	Kraken2 database (Directory or compressed tarball)

Outputs

record (
    meta: Record,
    special_meta: Record,
    kraken2_report: Path,
    scrub_report: Path?,
    classified: Set<Path?>,
    unclassified: Set<Path?>,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
special_meta	Record	A simplified metadata record for internal use
kraken2_report	Path	Standard Kraken2 report containing taxonomic abundance counts
scrub_report	Path?	Summary report of reads removed during host scrubbing
classified	Set<Path?>	Reads assigned to a taxon in the database (FASTQ)
unclassified	Set<Path?>	Reads NOT assigned to any taxon (FASTQ)
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 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

• kraken2 - Classify metagenomic reads using Kraken2.

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)

Source

View source on GitHub

Version

KRAKEN2:
    - bactopia-teton: 1.1.3