> For the complete documentation index, see [llms.txt](https://docs.opencga.opencb.org/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.opencga.opencb.org/manual/alignment-engine.md).

# Alignment Engine

- [BAM Index](https://docs.opencga.opencb.org/manual/alignment-engine/bam-index.md)
- [Alignment Read Query](https://docs.opencga.opencb.org/manual/alignment-engine/alignment-read-query.md)
- [Working with Coverage](https://docs.opencga.opencb.org/manual/alignment-engine/working-with-coverage.md)
- [Alignment Analysis](https://docs.opencga.opencb.org/manual/alignment-engine/alignment-analysis.md)