Qualimap is a Java application designed for quality control of next-generation sequencing (NGS) alignment data. It provides graphical and statistical analyses to evaluate the quality of sequence alignment data, which is crucial for identifying biases introduced by sequencing technologies, sample preparation, and mapping algorithms. Qualimap supports both BAM and count data, and allows users to analyze specific genomic regions of interest. The application processes alignment data by splitting the reference genome into windows, collecting information, and parallelizing the analysis. Results are visualized in charts and can be exported for further analysis. Qualimap also provides insights into mapping performance by analyzing read counts in relation to genomic features. Additionally, it includes tools for counting reads mapped to specific regions and clustering genomic features based on coverage profiles. Qualimap was tested on a plant resequencing dataset and a study on gene expression differences between human liver and kidney samples. It demonstrated its ability to detect coverage biases and identify enriched biotypes in mapped reads. Qualimap is freely available at http://www.qualimap.org. Funding was provided by the Spanish Ministry of Economy and Competitiveness and the EU-funded program ERA-NET PathoGenoMics. No conflicts of interest were declared.Qualimap is a Java application designed for quality control of next-generation sequencing (NGS) alignment data. It provides graphical and statistical analyses to evaluate the quality of sequence alignment data, which is crucial for identifying biases introduced by sequencing technologies, sample preparation, and mapping algorithms. Qualimap supports both BAM and count data, and allows users to analyze specific genomic regions of interest. The application processes alignment data by splitting the reference genome into windows, collecting information, and parallelizing the analysis. Results are visualized in charts and can be exported for further analysis. Qualimap also provides insights into mapping performance by analyzing read counts in relation to genomic features. Additionally, it includes tools for counting reads mapped to specific regions and clustering genomic features based on coverage profiles. Qualimap was tested on a plant resequencing dataset and a study on gene expression differences between human liver and kidney samples. It demonstrated its ability to detect coverage biases and identify enriched biotypes in mapped reads. Qualimap is freely available at http://www.qualimap.org. Funding was provided by the Spanish Ministry of Economy and Competitiveness and the EU-funded program ERA-NET PathoGenoMics. No conflicts of interest were declared.