SeqKit is a cross-platform, ultrafast toolkit designed for efficient manipulation of FASTA/Q files. It supports major operating systems including Windows, Linux, and Mac OSX, and can be used without any dependencies or pre-configurations. SeqKit offers a comprehensive set of functionalities, such as converting, searching, filtering, deduplication, splitting, shuffling, and sampling, with competitive performance in execution time and memory usage compared to similar tools. The toolkit is implemented in Go, leveraging high-performance bioinformatics packages for fast sequence parsing. It includes nineteen subcommands, each designed to handle specific tasks, and supports both plain and gzip-compressed inputs and outputs. SeqKit's efficiency is demonstrated through benchmark tests on various datasets, showing significant speed improvements over other tools like seqtk and biogo. The toolkit is open-source and available on GitHub, making it a valuable resource for researchers and bioinformatics users.SeqKit is a cross-platform, ultrafast toolkit designed for efficient manipulation of FASTA/Q files. It supports major operating systems including Windows, Linux, and Mac OSX, and can be used without any dependencies or pre-configurations. SeqKit offers a comprehensive set of functionalities, such as converting, searching, filtering, deduplication, splitting, shuffling, and sampling, with competitive performance in execution time and memory usage compared to similar tools. The toolkit is implemented in Go, leveraging high-performance bioinformatics packages for fast sequence parsing. It includes nineteen subcommands, each designed to handle specific tasks, and supports both plain and gzip-compressed inputs and outputs. SeqKit's efficiency is demonstrated through benchmark tests on various datasets, showing significant speed improvements over other tools like seqtk and biogo. The toolkit is open-source and available on GitHub, making it a valuable resource for researchers and bioinformatics users.