ArticleGenome research2025
Highly accurate assembly polishing with DeepPolisher.
Article in Genome research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
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- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- From contiguity to accuracy: Validation-centered perspectives on bacterial genome assembly.Journal of microbiology (Seoul, Korea) · 2026Review
- Haplotype-resolved genome assemblies of BJ and IMR-90 human fibroblast cell lines reveal extensive structural variation and enable reanalysis of historical sequencing data.Nucleic acids research · 2026Article
- A Complete Genome for the Common Marmoset.bioRxiv : the preprint server for biology · 2026Article
- Evaluating genome assemblies with HMM-Flagger.bioRxiv : the preprint server for biology · 2026Article
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- DL-GapFilling: a novel deep learning framework for improved plant genome gap filling.Briefings in bioinformatics · 2026Article
- Human acrocentric chromosome short armbioRxiv : the preprint server for biology · 2025Article
- Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance.bioRxiv : the preprint server for biology · 2025Article
- Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.bioRxiv : the preprint server for biology · 2025Article
- A complete diploid human genome benchmark for personalized genomics.bioRxiv : the preprint server for biology · 2025Article
- Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding.Genome research · 2025Article
- A Hitchhiker's Guide to long-read genomic analysis.Genome research · 2025Review
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14 authors.
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Abstract
Accurate genome assemblies are essential for biological research, but even the highest-quality assemblies retain errors caused by the technologies used to construct them. Base-level errors are typically fixed with an additional polishing step that uses reads aligned to the draft assembly to identify necessary edits. However, current methods struggle to find a balance between over- and underpolishing. Here, we present an encoder-only transformer model for assembly polishing called DeepPolisher, which predicts corrections to the underlying sequence using Pacific Biosciences (PacBio) HiFi read alignments to a diploid assembly. Our pipeline introduces a method, PHAsing Reads in Areas Of Homozygosity (PHARAOH), which uses ultralong Oxford Nanopore Technologies (ONT) data to ensure alignments are accurately phased and to correctly introduce heterozygous edits in falsely homozygous regions. We demonstrate that the DeepPolisher pipeline can reduce assembly errors by approximately half, mostly driven by reductions in indel errors. We have applied our DeepPolisher-based pipeline to 180 assemblies from the next Human Pangenome Reference Consortium (HPRC) data release, producing an average predicted quality value (QV) improvement of 3.4 (54% error reduction) for the majority of the genome.
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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.