|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:
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.
|Latest package for GNU Linux, MacOS and MS Windows:
Source code (GPL v.2)
Latest development snapshots
Public code repository
QualiMap Online User Manual
Sample data and output can be found here
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.
| Qualimap is a joint project of Max Planck Institute For Infection Biology and
of Centro de Investigación Príncipe Felipe (CIPF)
Konstantin Okonechnikov, Ana Conesa and Fernando García-Alcalde
"Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data."
btv566 (early access)
Fernando García-Alcalde et al. "Qualimap: evaluating next-generation sequencing alignment data." Bioinformatics 28, no. 20 (2012): 2678-2679.
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)