> For the complete documentation index, see [llms.txt](https://hq-1.gitbook.io/mc/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://hq-1.gitbook.io/mc/prepare.md).

# Prepare

- [Prepare PlateInfo & bcl2fastq SampleSheet](https://hq-1.gitbook.io/mc/prepare/inhouse-prepare-sample-sheet.md): Prepare bcl2fastq sample sheet for demultiplexing illumina primer index
- [Prepare Mapping Config](https://hq-1.gitbook.io/mc/prepare/prepare-mapping-config.md): Prepare a config file that contains all parameters and path to the genome reference
- [Prepare Reference Files](https://hq-1.gitbook.io/mc/prepare/prepare-mapping-config/prepare-reference-files.md)