kneaddata
KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments. In these experiments, samples are typically taken from a host in hopes of learning something about the microbial community on the host.
Detailed usage can be found here: https://huttenhower.sph.harvard.edu/kneaddata/
Link to section 'Versions' of 'kneaddata' Versions
- 0.10.0
Link to section 'Commands' of 'kneaddata' Commands
- kneaddata
- kneaddata_bowtie2_discordant_pairs
- kneaddata_build_database
- kneaddata_database
- kneaddata_read_count_table
- kneaddata_test
- kneaddata_trf_parallel
Link to section 'Module' of 'kneaddata' Module
You can load the modules by:
module load biocontainers
module load kneaddata
Link to section 'Example job' of 'kneaddata' 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 kneaddata on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=kneaddata
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers kneaddata
kneaddata --input examples/demo.fastq --reference-db examples/demo_db --output kneaddata_demo_outpu --threads 24 --processes 24