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

ABSTRACT:

Motivation

DNA CpG methylation (CpGm) has proven to be a crucial epigenetic factor in the mammalian 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 and implementation

An implementation of FAME is open source and licensed under GPL-3.0 at https://github.com/FischerJo/FAME.

SUBMITTER: Fischer J

PROVIDER: S-EPMC10310462 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature

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

Fischer Jonas J Schulz Marcel H MH

Bioinformatics (Oxford, England) 20230601 6

<h4>Motivation</h4>DNA CpG methylation (CpGm) has proven to be a crucial epigenetic factor in the mammalian gene regulatory system. Assessment of DNA CpG methylation values via whole-genome bisulfite sequencing (WGBS) is, however, computationally extremely demanding.<h4>Results</h4>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 meth ...[more]

PMID: 37326968

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