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Samtools vs Sambamba: catalog facts
Samtools	Sambamba
Best for: Researchers and developers working with high-throughput sequencing files	Best for: Genomics workflows that process SAM or BAM sequencing files
Free Free software under the MIT license.	Free Free and open source under GPL-2.0-or-later.
Command line	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	Parallel operations on SAM and BAM files Includes filtering, sorting, indexing and duplicate marking All 3 strengths for Sambamba Parallel operations on SAM and BAM files Includes filtering, sorting, indexing and duplicate marking Supports pipelines through standard input and output
A command-line tool intended for sequencing data workflows	Documented platform support is limited to Linux and macOS Requires the LDC compiler to build from source
Downloadable app	Downloadable app
Open source	Open source
License: MIT	License: GPL-2.0-or-later
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 Sambamba lomereiter.github.io/sambamba Catalog checked October 8, 2026

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