Jump to navigation Jump to search


seqkit website  

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.

This project describes 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.

Environment Modules

Run module spider seqkit to find out what environment modules are available for this application.

System Variables

  • HPC_SEQKIT_DIR - installation directory
  • HPC_SEQKIT_BIN - executable directory


If you publish research that uses seqkit you have to cite it as follows:

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation