Compare software

Seqtk vs Samtools: catalog facts
Seqtk	Samtools
Best for: Researchers processing FASTA or FASTQ sequencing data	Best for: Researchers and developers working with high-throughput sequencing files
Free Free and open source under the MIT license.	Free Free software under the MIT license.
Command line	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	Handles SAM, BAM and CRAM sequencing files Includes indexing and viewing operations All 3 strengths for Samtools Handles SAM, BAM and CRAM sequencing files Includes indexing and viewing operations Works alongside BCFtools for variant data
Requires building from source.	A command-line tool intended for sequencing data workflows
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 Samtools htslib.org Catalog checked October 8, 2026

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