Qualimap is a Java application designed for the quality control of next-generation sequencing (NGS) alignment data. It provides a user-friendly interface for analyzing SAM/BAM files, which contain information from tens to hundreds of millions of reads. The application supports both graphical and statistical analyses, helping to identify biases and issues in the sequencing and mapping processes. Qualimap can process BAM files by splitting the reference genome into windows, collecting and parallelizing information, and providing detailed results in various charts. It also offers tools for counting reads mapped to specific regions and clustering genomic features based on coverage profiles. The software is freely available at http://www.qualimap.org and has been demonstrated to effectively identify biases in plant resequencing and RNA-seq data.Qualimap is a Java application designed for the quality control of next-generation sequencing (NGS) alignment data. It provides a user-friendly interface for analyzing SAM/BAM files, which contain information from tens to hundreds of millions of reads. The application supports both graphical and statistical analyses, helping to identify biases and issues in the sequencing and mapping processes. Qualimap can process BAM files by splitting the reference genome into windows, collecting and parallelizing information, and providing detailed results in various charts. It also offers tools for counting reads mapped to specific regions and clustering genomic features based on coverage profiles. The software is freely available at http://www.qualimap.org and has been demonstrated to effectively identify biases in plant resequencing and RNA-seq data.