Compare software

SeqKit vs Samtools: catalog facts
SeqKit	Samtools
Best for: Researchers and bioinformatics users working with FASTA or FASTQ files	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.
Windows, macOS, Linux, Command line	Command line
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	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
Focused on FASTA and FASTQ sequence data	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 SeqKit bioinf.shenwei.me/seqkit 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.