SeqKit2 is the latest iteration of the widely used sequence analysis tool SeqKit, designed to meet the growing demands of high-throughput sequencing studies. It offers expanded functionality, performance optimizations, and support for additional compression methods. SeqKit2 retains its pragmatic subcommand architecture, adding 19 new subcommands, bringing the total to 38 across eight categories. These new subcommands include features such as amplicon processing, robust sequence record parsing, and real-time analysis capabilities. The tool also supports three additional compression formats: XZ, Zstandard, and Bzip2. Performance benchmarks show that SeqKit2 outperforms its predecessor and other tools like Bioawk, Seqtk, and SeqFu, while maintaining competitive runtimes. SeqKit2 enhances user-friendliness with features like autocomplete, progress bars, and improved error handling. The tool is actively maintained and regularly updated based on user feedback, making it a versatile and efficient choice for sequence and alignment processing in bioinformatics.SeqKit2 is the latest iteration of the widely used sequence analysis tool SeqKit, designed to meet the growing demands of high-throughput sequencing studies. It offers expanded functionality, performance optimizations, and support for additional compression methods. SeqKit2 retains its pragmatic subcommand architecture, adding 19 new subcommands, bringing the total to 38 across eight categories. These new subcommands include features such as amplicon processing, robust sequence record parsing, and real-time analysis capabilities. The tool also supports three additional compression formats: XZ, Zstandard, and Bzip2. Performance benchmarks show that SeqKit2 outperforms its predecessor and other tools like Bioawk, Seqtk, and SeqFu, while maintaining competitive runtimes. SeqKit2 enhances user-friendliness with features like autocomplete, progress bars, and improved error handling. The tool is actively maintained and regularly updated based on user feedback, making it a versatile and efficient choice for sequence and alignment processing in bioinformatics.