Revision as of 21:24, 6 December 2019 by Moskalenko (talk | contribs) (Text replacement - "#uppercase" to "uc")
Jump to navigation Jump to search


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


  • 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


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)