CloudASM: an ultra-efficient cloud-based pipeline for mapping allele-specific DNA methylation-Reference-Cited by-同舟云学术

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

Published:2020-03-02 Issue:11 Volume:36 Page:3558-3560
ISSN:1367-4803
Container-title:Bioinformatics
language:en
Short-container-title:

Author:

Dumont Emmanuel L P¹^ORCID,Tycko Benjamin¹²³,Do Catherine¹

Affiliation:

1. Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA

2. Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ 07110, USA

3. Lombardi Comprehensive Cancer, Center Georgetown University, Washington, DC 20007, USA

Abstract

Abstract Summary 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 Platform (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

Funder

National Institutes of Health

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Link

http://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaa149/32970871/btaa149.pdf

Reference11 articles.

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2. Mechanisms and disease associations of haplotype-dependent allele-specific DNA methylation;Do;Am. J. Hum. Genet,2016

3. Genetic–epigenetic interactions in cis: a major focus in the post-GWAS era;Do;Genome Biol,2017

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