What is it? How does it work? Features

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.

Supported types of experiments include:
  • Whole-genome sequencing
  • Whole-exome sequencing
  • RNA-seq (speical mode available)
  • ChIP-seq

Qualimap examines sequencing alignment data in SAM/BAM files according to the features of the mapped reads and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis.

Starting from version 2.0 Qualimap provides multi-sample comparison of alignment and counts data.
  • Fast analysis accross the reference of genome coverage and nucleotide distribution;
  • Easy to interpret summary of the main properties of the alignment data;
  • Analysis of the reads mapped inside/outside of the regions provided in GFF format;
  • Computation and analysis of read counts obtained from intersectition of read alignments with genomic features;
  • Analysis of the adequasy of the sequencing depth in RNA-seq experiments;
  • Multi-sample comparison of alignment and counts data;
  • Clustering of epigenomic profiles.
Download Documentation Support
Latest package for GNU Linux, MacOS and MS Windows:

Latest development snapshots

Public code repository

CIPF BioInfo local Maven repository

Version history
QualiMap Online User Manual

Sample data and output can be found here

Bioinformatics links:

Picard: a Java API (SAM-JDK) for creating programs that read and write SAM files.
FastQC: a quality control tool for high throughput sequence data.
SAMTools: essential utilities for manipulating alignments in the SAM format.
NOISeq: quality control and differential gene expression analysis for RNA-seq data.
Repitools: quality assessment, visualization, summarization and statistical analysis of epigenomics experiments.

Software development links:

JProfiler: an award-winning all-in-one Java performance profiler.
To get quick updates or report bugs/suggestions please join the QualiMap Google group:

Google Groups
Your email:

Contact Publications Funding
Qualimap is a joint project of Max Planck Institute For Infection Biology and Bioinformatics Department
of Centro de Investigación Príncipe Felipe (CIPF)

Konstantin Okonechnikov
Sonia Tarazona
Ana Conesa

Fernando Garcia-Alcalde
Konstantin Okonechnikov, Ana Conesa and Fernando García-Alcalde "Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data." Bioinformatics(2015)
btv566 (early access)

Fernando García-Alcalde et al. "Qualimap: evaluating next-generation sequencing alignment data." Bioinformatics 28, no. 20 (2012): 2678-2679.
doi: 10.1093/bioinformatics/bts503
BIO2009-10799 from the Spanish Ministry of Economy and Competitiveness and BIO2008-05266-E/- associated to the EU funded program ERA-NET PathoGenoMics.

Seventh Research Framework Programme of the European Union, Marie Curie Programme EIMID-IAPP (European Initiative for basic research in Microbiology and Infectious; PIAP-GA-2008-217768)

QualiMap screenshots:

Highslide JS
BAM QC: summary
Highslide JS
BAM QC: coverage across reference
Highslide JS
BAM QC: reference fraction coverage
Highslide JS
RNA-seq QC: coverage across gene body
Highslide JS
Counts QC: global saturation plot
Highslide JS
Multi-sample BAM QC: GC-content distribution