SAMtools

biotoolsVerifiedMaintained by Petr Danecek

v1.21…Docs available

A suite of programs for interacting with high-throughput sequencing data. SAMtools provides utilities for manipulating alignments in SAM/BAM/CRAM format, including sorting, merging, indexing, and generating per-position information.

nf-core OfficialBioContainersPublishedAdmin Reviewed

95trust score

FAIR

Homepage →View on bio.tools →License: MIT

GenomicsSequencingAlignmentFile manipulation

Use with AI

Install the MCP server or CLI to instantly fetch SAMtools documentation:

Install command

claude mcp add biocontext7 -- npx @biocontext7/mcp

Or share this page: biocontext7.com/tools/samtools

EDAM Annotations

Installation

conda

conda install -c bioconda samtools

brew

brew install samtools

Container Images

quay.io

docker pull quay.io/biocontainers/samtools:1.21--h50ea8bc_0

docker.io

docker pull docker.io/biocontainers/samtools:v1.21_cv1

Pipeline Integrations

nf-core/modules samtoolsnf-core

samtools/sortsnakemake-wrapper

Version History

v1.212024-09-12
Performance improvements, new markdup features
v1.202024-04-15
CRAM 3.1 support
v1.192024-01-10
v1.182023-08-25