SAMtools
Tools (written in C using htslib) for manipulating next-generation sequencing data
A foundational command-line toolkit for manipulating, analyzing, and converting SAM, BAM, and CRAM sequencing alignments.
About the Project
Why use this?
SAMtools provides core command-line utilities for working with high-throughput sequencing alignments. It supports viewing, sorting, indexing, filtering, merging, splitting, and converting SAM, BAM, and CRAM files, along with mpileup and variant-calling workflows through its tightly coordinated BCFtools project.
Genomics engineers choose SAMtools because it is a fast, stable, and universally supported foundation for sequencing pipelines. It is essential for alignment post-processing, coverage analysis, read filtering, variant discovery, and building reproducible genomics workflows on servers, HPC systems, and workflow engines. [283][292][293]
Key Features
- SAM, BAM, and CRAM manipulation and conversion
- Sorting, indexing, filtering, merging, and splitting alignments
mpileupand variant-calling integration with BCFtools- Fast C implementation built on htslib
- Standard foundation for reproducible sequencing pipelines
- Reference / Repo
- https://github.com/samtools/samtools
- Tool / Hosted
- https://samtools.github.io/
- Replaces / Alternative to
- Proprietary sequencing-alignment viewers and processing suites
- Free layer
- open-source