samtools/samtools

Health v2 · maintenance only

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1945 stars · 614 forks observed · 2026-08-28

What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded

SAMtools is a suite of C command-line programs, built on HTSlib, for reading, writing, editing, indexing, sorting, and viewing SAM/BAM/CRAM high-throughput sequencing files. It is the de facto standard toolkit for manipulating next-generation sequencing alignment data.

Use cases

• convert SAM files to BAM or CRAM format
• sort and index a BAM alignment file
• extract reads overlapping a genomic region from a BAM
• compute alignment statistics for a sequencing run
• call variants with mpileup
• mark PCR duplicates in aligned reads
• view and filter reads from a large BAM file

When to choose

• you work with SAM/BAM/CRAM sequencing data in genomics pipelines
• you need fast, memory-efficient command-line manipulation of alignment files
• you need a mature, widely cited tool for reproducible bioinformatics workflows

When to avoid

• you need a GUI for exploring alignments interactively
• you need VCF/BCF variant file manipulation (use bcftools instead)
• you need a library API for sequencing formats in your own code (use htslib directly)

Facets

cli-tool · maturity stable

cli parser file-system data-science bioinformatics developer-tools windows cpp cli sam bam cram genomics sequencing htslib variant-calling bioinformatics command-line linux macos

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markdown · JSON · MCP: product_card(name="samtools/samtools")