Compare software

Samtools vs Seqtk: catalog facts
Samtools	Seqtk
Best for: Researchers and developers working with high-throughput sequencing files	Best for: Researchers processing FASTA or FASTQ sequencing data
Free Free software under the MIT license.	Free Free and open source under the MIT license.
Command line	Command line
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	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
A command-line tool intended for sequencing data workflows	Requires building from source.
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 Samtools htslib.org Catalog checked October 8, 2026	Official website Full listing and sources Sources for Seqtk github.com/lh3/seqtk Catalog checked October 8, 2026

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