ArticleNAR genomics and bioinformatics2021
Fast and memory-efficient mapping of short bisulfite sequencing reads using a two-letter alphabet.
Article in NAR genomics and bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Sperm AluY Epimutations in Male Partners of Couples with Unexplained Recurrent Pregnancy Loss.bioRxiv : the preprint server for biology · 2026Article
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- Assessing the influence of different alignment tools on the accuracy of a forensic epigenetic clock.Bioinformatics (Oxford, England) · 2026Article
- Evolution of Gene Expression Across Functional Regions of the Mouse Placenta.Genome biology and evolution · 2026Article
- Neuronal hyperactivity becomes mTORC1 independent due to transcriptional changes in tuberous sclerosis complex disease models.Cell reports · 2025Article
- Multi-layered dosage compensation of the avian Z chromosome by increased transcriptional burst frequency and elevated translational rates.Nature communications · 2025Article
- Self-Reported Race as a Determinant of Differential Methylation in Peripheral Artery Disease.Circulation · 2025Article
- Aryana-bs: context-aware alignment of bisulfite-sequencing reads.BMC bioinformatics · 2025Article
- methylGrapher: genome-graph-based processing of DNA methylation data from whole genome bisulfite sequencing.Nucleic acids research · 2025Article
- BASAL: a universal mapping algorithm for nucleotide base-conversion sequencing.Nucleic acids research · 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
- Repetitive element transcript accumulation is associated with inflammaging in humans.GeroScience · 2024Article
- PRC2-AgeIndex as a universal biomarker of aging and rejuvenation.Nature communications · 2024Article
- Creating and Using Minimizer Sketches in Computational Genomics.Journal of computational biology : a journal of computational molecular cell biology · 2023Review
- Genome-wide methylation patterns from canine nanopore assemblies.G3 (Bethesda, Md.) · 2023Article
- Global effects of identity and aging on the human sperm methylome.Clinical epigenetics · 2023Article
- Strobealign: flexible seed size enables ultra-fast and accurate read alignment.Genome biology · 2022Article
- Benchmarking DNA methylation analysis of 14 alignment algorithms for whole genome bisulfite sequencing in mammals.Computational and structural biotechnology journal · 2022Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA cytosine methylation is an important epigenomic mark with a wide range of functions in many organisms. Whole genome bisulfite sequencing is the gold standard to interrogate cytosine methylation genome-wide. Algorithms used to map bisulfite-converted reads often encode the four-base DNA alphabet with three letters by reducing two bases to a common letter. This encoding substantially reduces the entropy of nucleotide frequencies in the resulting reference genome. Within the paradigm of read mapping by first filtering possible candidate alignments, reduced entropy in the sequence space can increase the required computing effort. We introduce another bisulfite mapping algorithm (abismal), based on the idea of encoding a four-letter DNA sequence as only two letters, one for purines and one for pyrimidines. We show that this encoding can lead to greater specificity compared to existing encodings used to map bisulfite sequencing reads. Through the two-letter encoding, the abismal software tool maps reads in less time and using less memory than most bisulfite sequencing read mapping software tools, while attaining similar accuracy. This allows
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Registered trials
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.