BamTools is a software suite designed to facilitate the analysis and management of BAM files, which are commonly used in genomic sequencing data. The suite includes a C++ API and a command-line toolkit, providing efficient and flexible tools for tasks such as filtering, merging, and sorting. The API offers intuitive interfaces for querying and generating BAM files, while the toolkit provides utilities for end-users to query and manipulate BAM files. Key features include an alternative indexing format (BTI) that improves access speed, scriptable filtering capabilities, and support for various data formats. BamTools has been integrated into several applications, including the BEDtools suite and the freeBayes variant caller, and has been successfully used in large-scale sequencing projects.BamTools is a software suite designed to facilitate the analysis and management of BAM files, which are commonly used in genomic sequencing data. The suite includes a C++ API and a command-line toolkit, providing efficient and flexible tools for tasks such as filtering, merging, and sorting. The API offers intuitive interfaces for querying and generating BAM files, while the toolkit provides utilities for end-users to query and manipulate BAM files. Key features include an alternative indexing format (BTI) that improves access speed, scriptable filtering capabilities, and support for various data formats. BamTools has been integrated into several applications, including the BEDtools suite and the freeBayes variant caller, and has been successfully used in large-scale sequencing projects.