samtools
A suite of command-line tools for manipulating SAM, BAM, and CRAM files in next-generation sequencing data analysis.
What is samtools?
Samtools is a suite of command-line utilities for manipulating and analyzing next-generation sequencing data stored in SAM, BAM, and CRAM formats. It provides essential tools for sorting, indexing, querying, and generating pileup data, forming a core component of genomic analysis pipelines. The project solves the need for efficient, reliable processing of large-scale sequencing datasets.
Bioinformaticians, genomic researchers, and data scientists working with high-throughput sequencing data who require robust command-line tools for data manipulation and analysis.
Developers choose Samtools for its proven reliability, extensive feature set, and tight integration with the HTSlib ecosystem. It is a standard tool in genomics with widespread adoption, offering performance-optimized utilities that are essential for professional sequencing pipelines.
Overview
Tools (written in C using htslib) for manipulating next-generation sequencing data
Use Cases
Best For
- Processing and converting SAM/BAM/CRAM files in genomic workflows
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