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Samtools vs SeqKit: catalog facts
Samtools	SeqKit
Best for: Researchers and developers working with high-throughput sequencing files	Best for: Researchers and bioinformatics users working with FASTA or FASTQ files
Free Free software under the MIT license.	Free Free and open source under the MIT license.
Command line	Windows, macOS, Linux, 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	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
A command-line tool intended for sequencing data workflows	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 Samtools htslib.org 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.