> For the complete documentation index, see [llms.txt](https://hq-1.gitbook.io/allcools/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/allcools/master.md).

# Before Start

## What is ALLCools?

### Developer

Hanqing Liu

## How to use it?

## Before ALLCools?

Check out [YAP](https://hq-1.gitbook.io/mc/), the mapping pipeline for data generated by the single-cell methylome based sequencing technologies. YAP deals with demultiplexing single-cell data and mapping FASTQ files to BAM and then generate the ALLC files.