Kneaddata

Introduction

Kneaddata is a tool designed to perform quality control on metagenomic sequencing data.

For more information, please check:

Docker hub: https://hub.docker.com/r/biobakery/kneaddata

Home page: http://huttenhower.sph.harvard.edu/kneaddata

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster	Version(s)
ANVIL	0.10.0
BELL	0.10.0
GAUTSCHI	0.10.0
NEGISHI	0.10.0
SCHOLAR	0.10.0

Commands

• kneaddata

• kneaddata_bowtie2_discordant_pairs

• kneaddata_build_database

• kneaddata_database

• kneaddata_read_count_table

• kneaddata_test

• kneaddata_trf_parallel

Module

You can load the modules by:

module load biocontainers
module load kneaddata

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 kneaddata on our clusters:

Anvil

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers kneaddata

# Your kneaddata workflow...

Bell, Gautschi, or Negishi

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers kneaddata

# Your kneaddata workflow...

Gautschi-AI

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers kneaddata

# Your kneaddata workflow...

Gilbreth

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers kneaddata

# Your kneaddata workflow...

Scholar

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers kneaddata

# Your kneaddata workflow...