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:
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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. |
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Download | Documentation | Support | |
Latest package for GNU Linux, MacOS and MS Windows: qualimap_v2.3.zip 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. |
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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) Team: Konstantin Okonechnikov Sonia Tarazona Ana Conesa Leader: 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) |