Difference between revisions of "QualiMap"

Jump to navigation Jump to search
m (Text replacement - "#uppercase" to "uc")
Line 1: Line 1:
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:GUI Apps]]

Revision as of 15:08, 6 June 2022


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)