Kraken2

Kraken 2 is a taxonomic classification system for metagenomics

Citation

Citation: 10.1186/s13059-019-1891-0

Environment

This tool uses the following conda environment:

Channels: - conda-forge - bioconda

Dependencies: - kraken2

Installation

This tool will be automatically installed when first used:

library(ShennongTools)

# Tool will be installed automatically on first use
result <- sn_run("kraken2", "classify", ...)

Available Commands

classify

Classify sequences against a Kraken2 database

Basic Usage:

result <- sn_run("kraken2", "classify",
  # Add your parameters here
)

build

Build or update a Kraken2 database

Basic Usage:

result <- sn_run("kraken2", "build",
  # Add your parameters here
)

Examples

Classify Example

library(ShennongTools)

result <- sn_run("kraken2", "classify",
  input = "input_file.txt",
  threads = 4
)

# Check if successful
if (sn_is_toolcall_success(result)) {
  cat("Command completed successfully!\n")
} else {
  cat("Command failed. Check logs:\n")
  cat(readLines(result@log_file), sep = "\n")
}

Build Example

library(ShennongTools)

result <- sn_run("kraken2", "build",
  db_dir = "example_file",
  threads = 4
)

# Check if successful
if (sn_is_toolcall_success(result)) {
  cat("Command completed successfully!\n")
} else {
  cat("Command failed. Check logs:\n")
  cat(readLines(result@log_file), sep = "\n")
}

Parameters Reference

classify Parameters

Inputs:

Parameter	Type	Required	Description
`input`	fastq, fasta	Yes	Input reads (single-end or paired-end)

Outputs:

Parameter	Type	Required	Description
`report`	tsv	No	Kraken2 classification report (with –report)
`output`	tsv	No	Classified output (with –output)

Parameters:

Parameter	Type	Default	Description
`db`	directory	“”	Path to Kraken2 database
`paired`	boolean	FALSE	Whether input is paired-end
`threads`	integer	4	Number of threads
`confidence`	numeric	0	Confidence threshold for classification
`extras`	string	“”	Additional arguments

build Parameters

Inputs:

Parameter	Type	Required	Description
`fasta`	fasta	No	Optional FASTA files for custom library

Outputs:

Parameter	Type	Required	Description
`db_dir`	directory	Yes	Output database directory

Parameters:

Parameter	Type	Default	Description
`db`	string	“kraken2_db”	Name of the Kraken2 database directory
`build_command`	string	“–build”	Kraken2 build subcommand (e.g., –download-library, –add-to-library, –build)
`taxon`	string	“”	NCBI taxonomy (e.g., bacteria, viral) for downloading
`threads`	integer	4	Number of threads
`extras`	string	“”	Extra options