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:

Source code (GPL v.2)

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