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Sambamba vs Samtools: catalog facts
Sambamba	Samtools

Best for: Genomics workflows that process SAM or BAM sequencing files	Best for: Researchers and developers working with high-throughput sequencing files
Free Free and open source under GPL-2.0-or-later.	Free Free software under the MIT license.
macOS, Linux, Command line	Command line
Parallel operations on SAM and BAM files Includes filtering, sorting, indexing and duplicate marking Supports pipelines through standard input and output	Handles SAM, BAM and CRAM sequencing files Includes indexing and viewing operations Works alongside BCFtools for variant data
Documented platform support is limited to Linux and macOS Requires the LDC compiler to build from source	A command-line tool intended for sequencing data workflows
Downloadable app	Downloadable app
Open source	Open source
License: GPL-2.0-or-later	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 Sambamba lomereiter.github.io/sambamba 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.