ArticleNature biotechnology2015
De novo sequencing and variant calling with nanopores using PoreSeq.
Article in Nature biotechnology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
37 citing papers in PubMed.
- Single-Molecule Bioelectronic Sensors with AI-Aided Data Analysis: Convergence and Challenges.Precision chemistry · 2024Review
- HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing.Genome biology · 2023Article
- Small Open Reading Frame-Encoded Micro-Peptides: An Emerging Protein World.International journal of molecular sciences · 2023Review
- Article
- KARGAMobile: Android app for portable, real-time, easily interpretable analysis of antibiotic resistance genesFrontiers in bioengineering and biotechnology · 2022Article
- InnovativeFrontiers in genetics · 2022Review
- Detection and Characterization of Single Cisplatin Adducts on DNA by Nanopore Sequencing.ACS omega · 2021Article
- Uncertainties in synthetic DNA-based data storage.Nucleic acids research · 2021Review
- Enabling nanopore technology for sensing individual amino acids by a derivatization strategy.Journal of materials chemistry. B · 2020Article
- Lifetime and Stability of Silicon Nitride Nanopores and Nanopore Arrays for Ionic Measurements.ACS nano · 2020Article
- Mitochondrial DNA alterations may influence the cisplatin responsiveness of oral squamous cell carcinoma.Scientific reports · 2020Article
- Solid-state nanopore fabrication by automated controlled breakdown.Nature protocols · 2020Article
- Athena: Automated Tuning of k-mer based Genomic Error Correction Algorithms using Language Models.Scientific reports · 2019Article
- Stable fabrication of a large nanopore by controlled dielectric breakdown in a high-pH solution for the detection of various-sized molecules.Scientific reports · 2019Article
- Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology.Plants (Basel, Switzerland) · 2019Article
- Next-Generation Sequencing in Acute Lymphoblastic Leukemia.International journal of molecular sciences · 2019Review
- Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables.Computational and structural biotechnology journal · 2019Review
- Design and MinION testing of a nanopore targeted gene sequencing panel for chronic lymphocytic leukemia.Scientific reports · 2018Article
- Two-step breakdown of a SiN membrane for nanopore fabrication: Formation of thin portion and penetration.Scientific reports · 2018Article
- Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing.The Journal of molecular diagnostics : JMD · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
The accuracy of sequencing single DNA molecules with nanopores is continually improving, but de novo genome sequencing and assembly using only nanopore data remain challenging. Here we describe PoreSeq, an algorithm that identifies and corrects errors in nanopore sequencing data and improves the accuracy of de novo genome assembly with increasing coverage depth. The approach relies on modeling the possible sources of uncertainty that occur as DNA transits through the nanopore and finds the sequence that best explains multiple reads of the same region. PoreSeq increases nanopore sequencing read accuracy of M13 bacteriophage DNA from 85% to 99% at 100× coverage. We also use the algorithm to assemble Escherichia coli with 30× coverage and the λ genome at a range of coverages from 3× to 50×. Additionally, we classify sequence variants at an order of magnitude lower coverage than is possible with existing methods.
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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.