Bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. It uses the taxonomic assignments made by Kraken 2 to estimate species- (or other level) abundances.

Bracken

License

Free to use and open source under GNU GPLv3.

Available

Roihu-CPU: 2.8, 2.9, via the bio-apps module.

Usage

Bracken is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the Bracken module:

module load bio-apps/v202603
module load bracken/2.9

Databases

Bracken works with a Kraken 2 database, which additionally needs a Bracken database built from it (with bracken-build). These reference databases are not bundled with the module.

Shared reference databases

CSC plans to provide shared reference databases at a central location on Roihu. This is still being set up. Until it is available, build or download your own in a writable location (for example your project's /scratch).

Running Bracken

After classifying reads with Kraken 2, estimate abundances at a given taxonomic level (for example species, -l S) with:

bracken -d /scratch/<project>/kraken_db -i sample.kreport -o sample.bracken -r 150 -l S

where -r is the read length and -d points to the Kraken 2 / Bracken database.

Example batch script

#!/bin/bash
#SBATCH --job-name=bracken
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=8G

module load bio-apps/v202603
module load bracken/2.9

bracken -d /scratch/<project>/kraken_db -i sample.kreport -o sample.bracken -r 150 -l S

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk