ArticleComputational and structural biotechnology journal2022
Benchmarking DNA methylation analysis of 14 alignment algorithms for whole genome bisulfite sequencing in mammals.
Article in Computational and structural biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 31 citations in OpenAlex.
- Mapping ovarian cellular and molecular landscape across the lifespan of women: a scoping review.Human reproduction update · 2026Article
- Assessing the influence of different alignment tools on the accuracy of a forensic epigenetic clock.Bioinformatics (Oxford, England) · 2026Article
- Exploring single-cell and multi-omics technologies and their role in unraveling tumor heterogeneity of hepatocellular carcinoma.Journal of liver cancer · 2026Review
- Estimation of DNA Methylation in Wheat Using Reverse Phase Ultra-High-Performance Liquid Chromatography Coupled with Mass Spectrometry During Leaf Rust Pathogenesis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Analysis Methods for Diagnosing Rare Neurodevelopmental Diseases with Episignatures: A Systematic Review of the Literature.Biomedicines · 2025Review
- Computational Workflow for Genome-Wide DNA Methylation Profiling and Differential Methylation Analysis.Bio-protocol · 2025Article
- Non-CG DNA methylation in animal genomes.Nature genetics · 2025Review
- Aryana-bs: context-aware alignment of bisulfite-sequencing reads.BMC bioinformatics · 2025Article
- Evaluation of Illumina and Oxford Nanopore Sequencing for the Study of DNA Methylation in Alzheimer's Disease and Frontotemporal Dementia.International journal of molecular sciences · 2025Review
- scRNA seq of an F1 cross of Marek's disease resistant and susceptible chickens identifies allele specific expression signatures enriched in transcription modulators.Scientific reports · 2025Article
- Benchmarking strategies for CNV calling from whole genome bisulfite data in humans.Computational and structural biotechnology journal · 2025Article
- Multi-metric locality sensitive hashing enhances alignment accuracy of bisulfite sequencing reads: BisHash.Bioinformatics advances · 2025Article
- Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform.BMC bioinformatics · 2023Article
- Exploring the crop epigenome: a comparison of DNA methylation profiling techniques.Frontiers in plant science · 2023Review
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Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole genome bisulfite sequencing (WGBS) is an essential technique for methylome studies. Although a series of tools have been developed to overcome the mapping challenges caused by bisulfite treatment, the latest available tools have not been evaluated on the performance of reads mapping as well as on biological insights in multiple mammals. Herein, based on the real and simulated WGBS data of 14.77 billion reads, we undertook 936 mappings to benchmark and evaluate 14 wildly utilized alignment algorithms from reads mapping to biological interpretation in humans, cattle and pigs: Bwa-meth, BSBolt, BSMAP, Walt, Abismal, Batmeth2, Hisat_3n, Hisat_3n_repeat, Bismark-bwt2-e2e, Bismark-his2, BSSeeker2-bwt, BSSeeker2-soap2, BSSeeker2-bwt2-e2e and BSSeeker2-bwt2-local. Specifically, Bwa-meth, BSBolt, BSMAP, Bismark-bwt2-e2e and Walt exhibited higher uniquely mapped reads, mapped precision, recall and F1 score than other nine alignment algorithms, and the influences of distinct alignment algorithms on the methylomes varied considerably at the numbers and methylation levels of CpG sites, the calling of differentially methylated CpGs (DMCs) and regions (DMRs). Moreover, we reported that BSMAP showed the highest accuracy at the detection of CpG coordinates and methylation levels, the calling of DMCs, DMRs, DMR-related genes and signaling pathways. These results suggested that careful selection of algorithms to profile the genome-wide DNA methylation is required, and our works provided investigators with useful information on the choice of alignment algorithms to effectively improve the DNA methylation detection accuracy in mammals.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.