ArticleCommunications biology2024
Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat.
Article in Communications biology, 2024. 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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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
15 citing papers in PubMed.
- Article
- Article
- Haplotype-aware long-read error correction.Algorithms for molecular biology : AMB · 2026Article
- Development of a stable low-copy mini F plasmid derivative for evaluating β-lactamase substrate specificity through antimicrobial susceptibility testing.Microbiology spectrum · 2026Article
- Barbell reveals and resolves demultiplexing and trimming issues in Nanopore data.Bioinformatics (Oxford, England) · 2026Article
- Complete genome sequence of a carbapenem-resistantMicrobiology resource announcements · 2026Article
- High-quality metagenome assembly from nanopore reads with nanoMDBG.Nature communications · 2026Article
- Nanopore sequencing enables highly accurate genotyping and identification of resistance determinants in key nosocomial pathogens.Microbial genomics · 2026Article
- Efficient near telomere-to-telomere assembly of Nanopore Simplex reads.bioRxiv : the preprint server for biology · 2025Article
- MicroRNAs in long COVID: roles, diagnostic biomarker potential and detection.Human genomics · 2025Review
- Review
- Pooled, Long-read Sequencing for Structural Variant Characterization in Schistosome Populations.Genome biology and evolution · 2025Article
- Tracking Antimicrobial Resistant Organisms Timely: a workflow validation study for successive core-genome SNP-based nosocomial transmission analysis.JAC-antimicrobial resistance · 2025Article
- Comparative evaluation of sequencing platforms: Pacific Biosciences, Oxford Nanopore Technologies, and Illumina for 16S rRNA-based soil microbiome profiling.Frontiers in microbiology · 2025Article
- Methods for telomere length measurement: an update on current technologies and emerging approaches.Frontiers in molecular biosciences · 2025Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Error self-correction is crucial for analyzing long-read sequencing data, but existing methods often struggle with noisy data or are tailored to technologies like PacBio HiFi. There is a gap in methods optimized for Nanopore R10 simplex reads, which typically have error rates below 2%. We introduce DeChat, a novel approach designed specifically for these reads. DeChat enables repeat- and haplotype-aware error correction, leveraging the strengths of both de Bruijn graphs and variant-aware multiple sequence alignment to create a synergistic approach. This approach avoids read overcorrection, ensuring that variants in repeats and haplotypes are preserved while sequencing errors are accurately corrected. Benchmarking on simulated and real datasets shows that DeChat-corrected reads have significantly fewer errors-up to two orders of magnitude lower-compared to other methods, without losing read information. Furthermore, DeChat-corrected reads clearly improves genome assembly and taxonomic classification.
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Registered trials
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