Twelve years of SAMtools and BCFtools

TL;DR

SAMtools and BCFtools are essential, widely-used tools for high-throughput sequencing data analysis, with over a decade of continuous development, numerous features, and extensive adoption in genomic research.

Contribution

This paper reviews twelve years of development, highlighting the tools' evolution, features, and widespread adoption in genomics workflows.

Findings

Over a million installations via Bioconda

Continuous development with new features added

Extensive use in genomic pipelines

Abstract

Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. Findings The first version appeared online twelve years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed over a million times via Bioconda. The source code and documentation are available from http://www.htslib.org.