Efficiently quantifying DNA methylation for bulk- and single-cell bisulfite data

  • Motivation DNA CpG methylation (CpGm) has proven to be a crucial epigenetic factor in the gene regulatory system. Assessment of DNA CpG methylation values via whole-genome bisulfite sequencing (WGBS) is, however, computationally extremely demanding. Results We present FAst MEthylation calling (FAME), the first approach to quantify CpGm values directly from bulk or single-cell WGBS reads without intermediate output files. FAME is very fast but as accurate as standard methods, which first produce BS alignment files before computing CpGm values. We present experiments on bulk and single-cell bisulfite datasets in which we show that data analysis can be significantly sped-up and help addressing the current WGBS analysis bottleneck for large-scale datasets without compromising accuracy. Availability An implementation of FAME is open source and licensed under GPL-3.0 at https://github.com/FischerJo/FAME.

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Author:Jonas Fischer, Marcel Holger SchulzORCiDGND
Parent Title (English):bioRxiv
Document Type:Preprint
Date of Publication (online):2023/01/27
Date of first Publication:2023/01/27
Publishing Institution:Universit├Ątsbibliothek Johann Christian Senckenberg
Release Date:2023/03/17
Page Number:10
Institutes:Medizin / Medizin
Dewey Decimal Classification:0 Informatik, Informationswissenschaft, allgemeine Werke / 00 Informatik, Wissen, Systeme / 004 Datenverarbeitung; Informatik
5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
6 Technik, Medizin, angewandte Wissenschaften / 61 Medizin und Gesundheit / 610 Medizin und Gesundheit
Licence (German):License LogoCreative Commons - CC BY-ND - Namensnennung - Keine Bearbeitungen 4.0 International