ArticleNucleic acids research2014
Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Assessing the influence of different alignment tools on the accuracy of a forensic epigenetic clock.Bioinformatics (Oxford, England) · 2026Article
- Integrated epigenomic and transcriptional profiling reveals genotype-specific adaptive reprogramming to drought stress in Brassica napus.BMC plant biology · 2026Article
- Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard.Nucleic acids research · 2025Article
- Aryana-bs: context-aware alignment of bisulfite-sequencing reads.BMC bioinformatics · 2025Article
- Mouse metastable epialleles are extremely rare.Nucleic acids research · 2025Article
- Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences.Bioinformatics (Oxford, England) · 2024Article
- DNA methylation landscape reveals GNAS as a decitabine-responsive marker in patients with acute myeloid leukemia.Neoplasia (New York, N.Y.) · 2024Article
- Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet.Genome biology · 2024Article
- Cell-free DNA methylome analysis for early preeclampsia prediction.Nature medicine · 2023Article
- DNA methylation landscape reveals LIN7A as a decitabine-responsive marker in patients with t(8;21) acute myeloid leukemia.Clinical epigenetics · 2023Article
- Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform.BMC bioinformatics · 2023Article
- A Cautionary Tale of Sexing by Methylation: Hybrid Bisulfite-Conversion Sequencing of Immunoprecipitated Methylated DNA inAnimals : an open access journal from MDPI · 2022Article
- Performance of methods to detect genetic variants from bisulphite sequencing data in a non-model species.Molecular ecology resources · 2022Article
- Benchmarking DNA methylation analysis of 14 alignment algorithms for whole genome bisulfite sequencing in mammals.Computational and structural biotechnology journal · 2022Article
- Analysis of Bisulfite Sequencing Data Using Bismark and DMRcaller to Identify Differentially Methylated Regions.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis.Briefings in bioinformatics · 2021Article
- Comprehensive Evaluation of Differential Methylation Analysis Methods for Bisulfite Sequencing Data.International journal of environmental research and public health · 2021Article
- Species-Specific Relationships between DNA and Chromatin Properties of CpG Islands in Embryonic Stem Cells and Differentiated Cells.Stem cell reports · 2021Article
- DNA methylation-driven EMT is a common mechanism of resistance to various therapeutic agents in cancer.Clinical epigenetics · 2020Article
- Performance of Mapping Approaches for Whole-Genome Bisulfite Sequencing Data in Crop Plants.Frontiers in plant science · 2020Article
Corrections and comments
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10 authors.
Funding
Abstract
Coupling bisulfite conversion with next-generation sequencing (Bisulfite-seq) enables genome-wide measurement of DNA methylation, but poses unique challenges for mapping. However, despite a proliferation of Bisulfite-seq mapping tools, no systematic comparison of their genomic coverage and quantitative accuracy has been reported. We sequenced bisulfite-converted DNA from two tissues from each of two healthy human adults and systematically compared five widely used Bisulfite-seq mapping algorithms: Bismark, BSMAP, Pash, BatMeth and BS Seeker. We evaluated their computational speed and genomic coverage and verified their percentage methylation estimates. With the exception of BatMeth, all mappers covered >70% of CpG sites genome-wide and yielded highly concordant estimates of percentage methylation (r(2) ≥ 0.95). Fourfold variation in mapping time was found between BSMAP (fastest) and Pash (slowest). In each library, 8-12% of genomic regions covered by Bismark and Pash were not covered by BSMAP. An experiment using simulated reads confirmed that Pash has an exceptional ability to uniquely map reads in genomic regions of structural variation. Independent verification by bisulfite pyrosequencing generally confirmed the percentage methylation estimates by the mappers. Of these algorithms, Bismark provides an attractive combination of processing speed, genomic coverage and quantitative accuracy, whereas Pash offers considerably higher genomic coverage.
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