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FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and
protein sequences. Common manipulations of FASTA/Q file include converting,
searching, filtering, deduplication, splitting, shuffling, and sampling.
Existing tools only implement some of these manipulations, and not particularly
efficiently, and some are only available for certain operating systems.
Furthermore, the complicated installation process of required packages and
running environments can render these programs less user friendly.
SeqKit is a cross-platform ultrafast comprehensive toolkit for FASTA/Q
processing. SeqKit provides executable binary files for all major operating
systems, including Windows, Linux, and Mac OS X, and can be directly used
without any dependencies or pre-configurations. SeqKit demonstrates competitive
performance in execution time and memory usage compared to similar tools. The
efficiency and usability of SeqKit enable researchers to rapidly accomplish
common FASTA/Q file manipulations.
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