Bracken

Introduction

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

Detailed usage can be found here: https://github.com/jenniferlu717/Bracken

Note

Inside the bracken container image, kraken2 was also installed. As a result, when you load bracken/2.6.1-py37, kraken version 2.1.1 will be automatically loaded. Please do not load kraken2 module together with bracken module to avaoid conflict.

Versions

  • 2.6.1

  • 2.7

Commands

  • bracken

  • bracken-build

  • combine_bracken_outputs.py

  • kraken2

  • kraken2-build

  • kraken2-inspect

  • combine_bracken_outputs.py

  • est_abundance.py

  • generate_kmer_distribution.py

Module

You can load the modules by:

module load biocontainers
module load bracken/2.6.1-py37

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run bracken on our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=bracken
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers bracken/2.6.1-py37

DATABASE=minikraken2_v2_8GB_201904_UPDATE
kraken2 --threads 24  --report kranken2.report --db $DATABASE --paired --classified-out cseqs#.fq SRR5043021_1.fastq SRR5043021_2.fastq
bracken -d  $DATABASE -i kranken2.report -o bracken_output -w bracken.report