krakentools
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files.
Detailed usage can be found here: https://github.com/jenniferlu717/KrakenTools
Link to section 'Versions' of 'krakentools' Versions
- 1.2
Link to section 'Commands' of 'krakentools' Commands
- alpha_diversity.py
- beta_diversity.py
- combine_kreports.py
- combine_mpa.py
- extract_kraken_reads.py
- filter_bracken.out.py
- fix_unmapped.py
- kreport2krona.py
- kreport2mpa.py
- make_kreport.py
- make_ktaxonomy.py
Link to section 'Module' of 'krakentools' Module
You can load the modules by:
module load biocontainers
module load krakentools/1.2
Link to section 'Example job' of 'krakentools' 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 krakentools on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=krakentools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers krakentools/1.2
extract_kraken_reads.py -k myfile.kraken -t 2 -s1 SRR5043021_1.fastq -s2 SRR5043021_2.fastq -o extracted1.fq -o2 extracted2.fq