software:topical:lifescience:qa

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Quality Assessment of NGS Data

Checking the quality1) of experimental data is crucial to data analysis.

One of the best-known tools for estimating the sequencing quality (and providing summary statistics and plots) is FastQC.

We provide this software as modules under:

bio/FastQC

You can find a wrapper to ease your workflow, below.

We provide a wrapper module on Mogon in order to aggregate jobs and to integrate the quality check into a workflow.

The wrapper script is available as a module:

bio/parallel_QATools

The code is under version management and hosted internally, here.

The wrapper script will submit a job, it is not intended to be just within a SLURM environment, but rather creates one.

Calling QAWrapper -h will display a help message with all the options, the script provides. Likewise, the call QAWrapper –credits will display credits and a version history.

The script, after loading the module, can then be run like:

$ QAWrapper --executable=<executable> [options] <inputdir>

The current release only supports FastQC. Therefore, the –executable is meaningless.

About Arguments:

* inputdir needs to be a (relative) path to a directory containing all inputs. Subdirectories and files containing the string unpaired are ignored; this is to support preprocessing with the trimmomatic module.

The options:

  • QAWrapper attempts to deduce your SLURM account. This may fail, in which case -A, –account needs to be supplied.
  • -l,–runlimit, this defaults to 300 minutes.
  • -p,–partition, the default is nodeshort or parallel on Mogon2, no smp-partition should be choosen.
  • –args, arguments otherwise not set by the wrapper - the defaults of the choosen executable apply for unset arguments
  • -d,–dependency, list of comma separated jobids, the job will wait for to finish
  • -o,–outdir, output directory path (default is the current working directory)
  • –constraint, on Mogon II, only: defaults to broadwell

Output:

  • One analysis per input as specified by the respective executable.

1)
Quality checks or assessments are different to quality control or enhancement.
  • software/topical/lifescience/qa.1546952513.txt.gz
  • Last modified: 2019/01/08 14:01
  • by meesters