.. _backbone-label:

###########
 Kneaddata
###########

**************
 Introduction
**************

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

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 Versions
**********

-  0.12.0

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 Commands
**********

-  kneaddata
-  kneaddata_bowtie2_discordant_pairs
-  kneaddata_build_database
-  kneaddata_database
-  kneaddata_read_count_table
-  kneaddata_test
-  kneaddata_trf_parallel

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 Example job
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Adjust slurm options based on job requirements (`slurm cheat sheet
<https://slurm.schedmd.com/pdfs/summary.pdf>`_):

.. code::

   #!/bin/bash
   #SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
   #SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
   #SBATCH -N 1   # Number of nodes
   #SBATCH -n 1   # Number of tasks per node
   #SBATCH -c 4   # Number of CPU cores per task
   #SBATCH --mem=8G       # Memory required per node
   #SBATCH --job-name=kneaddata   # Job name
   #SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
   #SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
   #SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
   #SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

   module purge   ### Optional, but highly recommended.
   module load kneaddata/XXXX     ### Latest version is recommended.