In this major update, we present NGS-Pipeline 1.0.0, our first official release. This release includes a comprehensive set of tools for genome assembly and quality assessment, improving the performance and efficiency of genomic data processing. We have introduced new features to fine-tune the trimming process, dynamically build preprocessing commands, and provide full compatibility with a variety of computing environments. NGS-Pipeline 1.0 makes analysing genomic data easier by providing a more intuitive and accessible user interface.