CloudASM: an ultra-efficient cloud-based pipeline for mapping allele-specific DNA methylation.
basic_science · Level V
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- Record sourced from PubMed, PMID 32119067.
- Also identified by DOI 10.1093/bioinformatics/btaa149 and PMC identifier 7267820.
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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 Platform (GCP) that uses a novel pipeline manager and GCP's serverless enterprise data warehouse. 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. emmanuel.dumont@hmh-cdi.org.
Medical subject headings
- DNA Methylation
- Software