The article introduces PRINSEQ, an open-source application designed for quality control and preprocessing of genomic and metagenomic datasets. PRINSEQ provides tools to generate summary statistics, filter, reformat, and trim sequences, enhancing downstream analysis. It supports various quality metrics such as sequence complexity, dinucleotide odds ratio, and tag sequence probability. The software offers both a web interface and a standalone version, making it accessible to researchers with varying levels of expertise. Compared to other programs like SolexaQA, FastQC, and FASTX-Toolkit, PRINSEQ stands out for its comprehensive feature set and user-friendly interface. The tool is particularly useful for identifying and removing low-quality sequences, artifacts, and contaminants, ensuring the reliability of downstream analyses.The article introduces PRINSEQ, an open-source application designed for quality control and preprocessing of genomic and metagenomic datasets. PRINSEQ provides tools to generate summary statistics, filter, reformat, and trim sequences, enhancing downstream analysis. It supports various quality metrics such as sequence complexity, dinucleotide odds ratio, and tag sequence probability. The software offers both a web interface and a standalone version, making it accessible to researchers with varying levels of expertise. Compared to other programs like SolexaQA, FastQC, and FASTX-Toolkit, PRINSEQ stands out for its comprehensive feature set and user-friendly interface. The tool is particularly useful for identifying and removing low-quality sequences, artifacts, and contaminants, ensuring the reliability of downstream analyses.