Difference between revisions of "QualiMap"

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==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
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WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
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Available tools:
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*bamqc - Evaluate NGS mapping to a reference genome
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*rnaseq - Evaluate RNA-seq alignment data
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*counts - Counts data analysis (further RNA-seq data evaluation)
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*multi-bamqc - Compare QC reports from multiple NGS mappings
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*clustering - Cluster epigenomic signals
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*comp-counts - Compute feature counts
  
 
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Latest revision as of 21:24, 6 December 2019

Description

qualimap website  

Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.

Required Modules

Serial

  • qualimap

System Variables

  • HPC_QUALIMAP_DIR - installation directory

Additional Information

Available tools:

  • bamqc - Evaluate NGS mapping to a reference genome
  • rnaseq - Evaluate RNA-seq alignment data
  • counts - Counts data analysis (further RNA-seq data evaluation)
  • multi-bamqc - Compare QC reports from multiple NGS mappings
  • clustering - Cluster epigenomic signals
  • comp-counts - Compute feature counts



Citation

If you publish research that uses qualimap you have to cite it as follows:

Konstantin Okonechnikov, Ana Conesa and Fernando García-Alcalde "Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data." Bioinformatics(2015)