> For the complete documentation index, see [llms.txt](https://docs.imaps.goodwright.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.imaps.goodwright.com/fundamentals/genomes.md). # Genomes Many Bioinformatics workflows require aligning things to genomes, or some kind of genome 'context' in which to operate. iMaps therefore provides reference genomes for common model organisms, which can be easily selected when running these pipelines. The files for a genome are generated by the Prepare Genome pipeline. Each species will have one 'reference genome' - the public, iMaps-provided default version for that species - and there may be others that can be used as well. Anyone can run the Prepare Genome pipeline to generate versions of those genomes that are best suited to your research if the defaults do not suffice. --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://docs.imaps.goodwright.com/fundamentals/genomes.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.