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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.

Environment Modules

Run module spider qualimap to find out what environment modules are available for this application.

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


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)