software:topical:lifescience:qa

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Quality Assessment of NGS Data

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

FastQC

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.

You can visualize the html-files created by FastQC with firefox, which is installed on both clusters.

MultiQC External Linkis an assessment tool to gather the output of multiple quality indicators and to visualize them.

It is available as a module file:

bio/MultiQC

It can be run in a job to complete a pipeline with a quality assessment.

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.1548066345.txt.gz
  • Last modified: 2019/01/21 11:25
  • by meesters