CloudASM: an ultra-efficient cloud-based pipeline for mapping allele-specific DNA methylation

Abstract

Methods for quantifying the imbalance in CpG methylation between alleles genome-wide have been described but their algorithmic time complexity is quadratic and their practical use requires painstaking attention to infrastructure choice, implementation, and execution. To solve this problem, we developed CloudASM, a scalable, ultra-efficient, turn-key, portable pipeline on Google Cloud Computing (GCP) that uses a novel pipeline manager and GCP's serverless enterprise data warehouse. Availability and Implementation: CloudASM is freely available in the GitHub repository https://github.com/TyckoLab/CloudASM and a sample dataset and its results are also freely available at https://console.cloud.google.com/storage/browser/cloudasm. Contact: emmanuel.dumont@hmh-cdi.org Supplementary information: None.