Compare software

Seqtk vs SeqKit: catalog facts
Seqtk	SeqKit
Best for: Researchers processing FASTA or FASTQ sequencing data	Best for: Researchers and bioinformatics users working with FASTA or FASTQ files
Free Free and open source under the MIT license.	Free Free and open source under the MIT license.
Command line	Windows, macOS, Linux, Command line
Works with FASTA and FASTQ, including gzip-compressed files Includes conversion, trimming, extraction and sampling commands All 3 strengths for Seqtk Works with FASTA and FASTQ, including gzip-compressed files Includes conversion, trimming, extraction and sampling commands Has only zlib as a library dependency	Offers many commands for sequence-file operations Reads FASTA and FASTQ plus several compressed formats All 3 strengths for SeqKit Offers many commands for sequence-file operations Reads FASTA and FASTQ plus several compressed formats Supports standard input and output for shell pipelines
Requires building from source.	Focused on FASTA and FASTQ sequence data
Downloadable app	Downloadable app
Open source	Open source
License: MIT	License: MIT
Not stated if an account is needed	Not stated if an account is needed
Not stated if it works offline	Not stated if it works offline
Official website Full listing and sources Sources for Seqtk github.com/lh3/seqtk Catalog checked October 8, 2026	Official website Full listing and sources Sources for SeqKit bioinf.shenwei.me/seqkit Catalog checked October 8, 2026

“Not stated” means we have not confirmed it. Features can vary by device and plan.