bracken
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
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 avoid conflict.
Link to section 'Versions' of 'bracken' Versions
- 2.6.1
- 2.7
Link to section 'Commands' of 'bracken' Commands
- bracken
- bracken-build
- combine_bracken_outputs.py
- kraken2
- kraken2-build
- kraken2-inspect
- combine_bracken_outputs.py
- est_abundance.py
- generate_kmer_distribution.py
Link to section 'Module' of 'bracken' Module
You can load the modules by:
module load biocontainers
module load bracken/2.6.1-py37
Link to section 'Example job' of 'bracken' Example job
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