ArticleNature biotechnology2023
DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers.
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Who cites it
114 citing papers in PubMed, 146 citations in OpenAlex.
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- Z-Calling: a tool for A/Z (2,6-diaminopurine) base calling and dZ-DNA detection using PacBio HiFi reads.Communications biology · 2026Article
- Evaluating genome assemblies with HMM-Flagger.bioRxiv : the preprint server for biology · 2026Article
- Transcriptomic Regulation of Aquaporins During Seed Germination in the Marine SeagrassPlants (Basel, Switzerland) · 2026Article
- The functional landscape of coding variation in the familial hypercholesterolemia geneScience (New York, N.Y.) · 2026Article
- Chromosome-level genome assembly of the Gerbera (Gerbera hybrida) using HiFi long-read and Hi-C technologies.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Complete transition from chromosomal to cytoplasmic sex determination during prolonged Wolbachia symbiosis.Nature communications · 2026Article
- DL-GapFilling: a novel deep learning framework for improved plant genome gap filling.Briefings in bioinformatics · 2026Article
54 more citing papers are in PubMed but not listed here.
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Authors and funding
19 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Circular consensus sequencing with Pacific Biosciences (PacBio) technology generates long (10-25 kilobases), accurate 'HiFi' reads by combining serial observations of a DNA molecule into a consensus sequence. The standard approach to consensus generation, pbccs, uses a hidden Markov model. We introduce DeepConsensus, which uses an alignment-based loss to train a gap-aware transformer-encoder for sequence correction. Compared to pbccs, DeepConsensus reduces read errors by 42%. This increases the yield of PacBio HiFi reads at Q20 by 9%, at Q30 by 27% and at Q40 by 90%. With two SMRT Cells of HG003, reads from DeepConsensus improve hifiasm assembly contiguity (NG50 4.9 megabases (Mb) to 17.2 Mb), increase gene completeness (94% to 97%), reduce the false gene duplication rate (1.1% to 0.5%), improve assembly base accuracy (Q43 to Q45) and reduce variant-calling errors by 24%. DeepConsensus models could be trained to the general problem of analyzing the alignment of other types of sequences, such as unique molecular identifiers or genome assemblies.
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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.