software:topical:lifescience:qa

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software:topical:lifescience:qa [2019/03/12 09:02]
meesters
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-====== Quality Assessment of NGS Data ====== 
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-Checking the quality((Quality checks or assessments are different to quality control or enhancement.)) of experimental data is crucial to data analysis. 
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-===== Software Options ===== 
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-==== Individual Assessment Tools ==== 
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-=== FastQC === 
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-One of the best-known tools for estimating the sequencing quality (and providing summary statistics and plots) is [[https://www.bioinformatics.babraham.ac.uk/projects/fastqc/|FastQC]]. 
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-We provide this software as [[:setting_up_environment_modules|modules]] under: 
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-''bio/FastQC'' 
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-You can find a wrapper to ease your workflow, [[software:topical:lifescience:qa#the_wrapper_module_on_mogon|below]]. 
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-<WRAP center round info 90%> 
-You can visualize the html-files created by FastQC with ''firefox'', which is installed on both clusters. 
-</WRAP> 
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-==== Meta Assessment Tools ==== 
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-[[https://multiqc.info/|MultiQC]] is an assessment tool to gather the output of multiple quality indicators and to visualize them. 
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-It is available as a module file: 
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-''bio/MultiQC'' 
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-It can be run in a job to complete a pipeline with a quality assessment. 
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-===== The Wrapper Module on Mogon ===== 
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-We provide a wrapper module on Mogon in order to aggregate jobs and to integrate the quality check into a workflow. 
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-The wrapper script is available as a [[:setting_up_environment_modules|module]]: 
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-''bio/parallel_QATools'' 
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-The code is under version management and hosted internally, [[https://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis|here]]. 
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-<WRAP center round important 90%> 
-The wrapper script will submit a job, it is not intended to be just within a SLURM environment, but rather creates one. 
-</WRAP> 
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-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. 
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-The script, after loading the module, can then be run like: 
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-<code bash> 
-$ QAWrapper --executable=<executable> [options] <inputdir> 
-</code> 
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-<WRAP center round info 90%> 
-The current release only supports FastQC. Therefore, the ''--executable'' is meaningless. 
-</WRAP> 
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-About Arguments: 
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-  * ''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 [[software:topical:lifescience:qa|quality assessment module]]. 
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-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'' 
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-Output: 
-  * One analysis per input as specified by the respective executable. 
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  • Last modified: 2019/03/12 09:02
  • by meesters