Trimmomatic is a flexible and efficient preprocessing tool for Illumina sequence data, designed to handle paired-end data and meet the requirements of high-performance and correct handling of technical sequences such as adapters. The tool includes various processing steps for read trimming and filtering, with key innovations in adapter sequence identification and quality filtering. Trimmomatic offers two main quality filtering methods: Sliding Window and Maximum Information, which balance the retention of high-quality bases with the length of the read. The tool's performance is demonstrated through reference-based alignment using Bowtie 2 and BWA, and de novo assembly using Velvet, showing significant improvements in alignment rates and contig sizes. Compared to existing tools, Trimmomatic outperforms them in both reference-based and de novo assembly scenarios, particularly in strict alignment settings and with poor-quality data.Trimmomatic is a flexible and efficient preprocessing tool for Illumina sequence data, designed to handle paired-end data and meet the requirements of high-performance and correct handling of technical sequences such as adapters. The tool includes various processing steps for read trimming and filtering, with key innovations in adapter sequence identification and quality filtering. Trimmomatic offers two main quality filtering methods: Sliding Window and Maximum Information, which balance the retention of high-quality bases with the length of the read. The tool's performance is demonstrated through reference-based alignment using Bowtie 2 and BWA, and de novo assembly using Velvet, showing significant improvements in alignment rates and contig sizes. Compared to existing tools, Trimmomatic outperforms them in both reference-based and de novo assembly scenarios, particularly in strict alignment settings and with poor-quality data.