# samtools/samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

Repository: https://github.com/samtools/samtools
Canonical: https://ross.abutalabs.com/products/samtools
Homepage: http://htslib.org/
Language: C
License: NOASSERTION
License Family: other
Last push: 2026-08-21T14:14:59+00:00

## Health v2 (maintenance only)
Score: 96/100 (v2, computed 2026-09-02T17:46:02.011165+00:00)
- activity 98, release rhythm 92, longevity 100
- inputs: {"age_days": 5290, "days_push": 12, "days_rel": 54, "gap_med": 22.5, "n_releases_24m": 11}
- flags: no_license
- formula: round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10)

## Adoption (not part of the score)
Stars 1945, forks 614 (observed 2026-08-28T04:05:57.666033+00:00)

## What it is
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
- artifact type: cli-tool
- maturity: stable
- function: cli, parser, file-system, data-science
- domain: bioinformatics, developer-tools
- platform: windows, cpp, cli
- tags: sam, bam, cram, genomics, sequencing, htslib, variant-calling, bioinformatics, command-line, linux, macos

## Member repositories
- samtools/samtools (main) score 96

## Provenance
- Observed fields: from GitHub, fetched 2026-08-28T04:05:57.666033+00:00.
- Health v2: computed from the inputs above; adoption is never an input.
- Inferred fields (summary, facets, guidance): AI-extracted, prompt v1, taxonomy v1, on 2026-08-30T03:07:58.752209+00:00, confidence not recorded.
  - readme: https://github.com/samtools/samtools (fetched 2026-08-28T04:05:57.666033+00:00, sha dde923ec3f10)
  - homepage: http://htslib.org/ (fetched 2026-08-29T10:47:02.198863+00:00, sha 20f48e5195de)
  - site_page: https://www.htslib.org/doc (fetched 2026-08-29T10:47:02.207772+00:00, sha c0803321c06c)
- Data as of 2026-08-30T08:39:29.467469+00:00.