CloudASM: an ultra-efficient cloud-based pipeline for mapping allele-specific DNA methylation.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 06 2020
01 06 2020
Historique:
received:
19
11
2019
revised:
28
01
2020
accepted:
25
02
2020
pubmed:
3
3
2020
medline:
30
10
2020
entrez:
3
3
2020
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 32119067
pii: 5771329
doi: 10.1093/bioinformatics/btaa149
pmc: PMC7267820
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
3558-3560Subventions
Organisme : NIAID NIH HHS
ID : R21 AI133140
Pays : United States
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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