This repository contains the scripts used to align and process whole-genome bisulfite sequenced data collected on ~300 patients: one third with late-onset Alzheimer's disease, one-third with mild cognitive impairment, and one-third healthy.

Link incoming...

As much as possible, we use one conda environment, which can be created on your device with conda create --name load --file=load.yml

Most code is run on a cluster of servers which run Scientific Linux 7.9 (Nitrogen), which is based on Red Hat.

Environments are managed through MiniConda.

To process we use the gemBS pipeline, with some checking with bismark. We also use GNU parallel whenever possible.

Organization of this repository is based in part on (that bioinformatics paper).