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De novo Nanopore read quality improvement using deep learning

Nathan LaPierre, Rob Egan, Wei Wang, Zhong Wang
2019 BMC Bioinformatics  
MiniScrub is able to robustly improve read quality of Oxford Nanopore reads, especially in the metagenome setting, making it useful for downstream applications such as de novo assembly.  ...  Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification.  ...  Conclusions MiniScrub is a novel deep learning method for improving Nanopore read quality.  ... 
doi:10.1186/s12859-019-3103-z pmid:31694525 pmcid:PMC6833143 fatcat:3vgqrnoyqbdh7ij2rhfxbzb7tu

MiniScrub: de novo long read scrubbing using approximate alignment and deep learning [article]

Nathan LaPierre, Rob Egan, Wei Wang, Zhong Wang
2018 bioRxiv   pre-print
We developed a novel Convolutional Neural Network (CNN) based method, called MiniScrub, for de novo identification and subsequent "scrubbing" (removal) of low-quality Nanopore read segments.  ...  Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification.  ...  DE-AC02-05CH11231. The work conducted by Nathan LaPierre and Wei Wang was supported by NSF grant DGE-1829071 and NIH grants 5T32EB016640-05 and 4T32EB016640-04.  ... 
doi:10.1101/433573 fatcat:5xr56ko22vdh3obqqxjrgodkhm

MinCall - MinION end2end convolutional deep learning basecaller [article]

Neven Miculinić, Marko Ratković, Mile Šikić
2019 arXiv   pre-print
The best performing deep learning model achieves 91.4% median match rate on E. Coli dataset using R9 pore chemistry and 1D reads.  ...  The model is based on deep learning and uses convolutional neural networks (CNN) in its implementation.  ...  Consensus from de novo assembly In this evaluation method, the consensus sequence is calculated using de novo genome assembly.  ... 
arXiv:1904.10337v1 fatcat:7tq5hnsx6vgmfhmdqzx2f7lmm4

CONNET: Accurate Genome Consensus in Assembling Nanopore Sequencing Data via Deep Learning

Yifan Zhang, Chi-Man Liu, Henry CM. Leung, Ruibang Luo, Tak-Wah Lam
2020 iScience  
Single-molecule sequencing technologies produce much longer reads compared with next-generation sequencing, greatly improving the contiguity of de novo assembly of genomes.  ...  In this study, we discovered that the spatial relationship of alignment pileup is crucial to high-quality consensus and developed a deep learning-based consensus tool, CONNET, which outperforms the fastest  ...  Introduction Single-molecule sequencing (SMS) technologies produce much longer reads compared to next-generation sequencing, greatly improving the contiguity of de novo assembly of genomes.  ... 
doi:10.1016/j.isci.2020.101128 pmid:32422594 pmcid:PMC7229283 fatcat:lol4cne7lzfehe5c2yt53emiom

Nanopore sequencing data analysis: state of the art, applications and challenges

Alberto Magi, Roberto Semeraro, Alessandra Mingrino, Betti Giusti, Romina D'Aurizio
2017 Briefings in Bioinformatics  
Our analyses demonstrate that the use of nanopore data dramatically improves the de novo assembly of genomes and allows for the exploration of structural variants with an unprecedented accuracy and resolution  ...  Despite the short period of time from the release of the MinION, a large number of algorithms and tools have been developed for base calling, data handling, read mapping, de novo assembly and variant discovery  ...  In May 2016, ONT introduced the new R9 chemistry based on the protein nanopore CsgG, a novel algorithm for base calling that uses deep learning and the 'fast mode' that allows to sequence 250 bases/second  ... 
doi:10.1093/bib/bbx062 pmid:28637243 fatcat:lxiyn4exdfaibf4helkij43p2q

Towards Inferring Nanopore Sequencing Ionic Currents from Nucleotide Chemical Structures [article]

HONGXU DING, Ioannis Anastopoulos, Andrew D Bailey, Benedict Paten, Josh Stuart
2020 bioRxiv   pre-print
The characteristic ionic currents of nucleotide kmers are commonly used in analyzing nanopore sequencing readouts.  ...  We present a graph convolutional network-based deep learning framework for predicting kmer characteristic ionic currents from corresponding chemical structures.  ...  Such generalization of chemical information is a reason for optimism about the potential for de novo detection of nucleotide modifications. RESULTS Architecture of the deep learning framework.  ... 
doi:10.1101/2020.11.30.404947 fatcat:phzccioc4zfy5a6vjpo7lc5i3u

The blooming of long-read sequencing reforms biomedical research

Kin Fai Au
2022 Genome Biology  
The new software phasebook adapts a divide-and-conquer strategy to improve the coverage of haplotyperesolved de novo genome assembly [3] .  ...  For example, Xue et al. used PacBio HiFi reads to create a high-quality and nearly gap-free  ...  Barbara Cheifet for critically reading and editing the manuscript.  ... 
doi:10.1186/s13059-022-02604-2 pmid:35022055 pmcid:PMC8756655 fatcat:hlibqrqhfrdb7cintfn5lir76e

Third-generation sequencing and the future of genomics [article]

Hayan Lee, James Gurtowski, Shinjae Yoo, Maria Nattestad, Shoshana Marcus, Sara Goodwin, W. Richard McCombie, Michael Schatz
2016 bioRxiv   pre-print
We analyze how increased read lengths can be used to address long-standing problems in de novo genome assembly, structural variation analysis and haplotype phasing.  ...  Third-generation long-range DNA sequencing and mapping technologies are creating a renaissance in high-quality genome sequencing.  ...  as very high quality de novo assemblies of entire human genomes 16 .  ... 
doi:10.1101/048603 fatcat:buwxgaaj2fg2re2m3xegmshcu4

DeepSimulator: a deep simulator for Nanopore sequencing

Yu Li, Renmin Han, Chongwei Bi, Mo Li, Sheng Wang, Xin Gao, Bonnie Berger
2018 Bioinformatics  
Results: Here we propose a deep learning based simulator, DeepSimulator, to mimic the entire pipeline of Nanopore sequencing.  ...  Two case studies demonstrate the application of DeepSimulator to benefit the development of tools in de novo assembly and in low coverage SNP detection.  ...  Coin, Louise Roddam and Tania Duarte from University of Queensland for providing the nanopore sequencing data for the lambda phage, E. coli and Pandoraea pnomenusa samples.  ... 
doi:10.1093/bioinformatics/bty223 pmid:29659695 fatcat:hi7acxx5mrcnraw4j4hfldrnbm


Amada El-Sabeh
2021 Journal of Experimental and Molecular Biology  
The MinION's applications, potential and limitations are reviewed, focusing on its utility for bacterial genome de novo or hybrid assembly.  ...  Here, Oxford Nanopore Technology's MinION, the first handheld nanopore sequencing device, is evaluated in comparison with competing sequencing platforms.  ...  The use of nanopore sequencing greatly improves de novo genome assemblies when considering N50, contig numbers and its robustness with extreme GC content organisms, allowing the detection and exploration  ... 
doi:10.47743/jemb-2021-57 fatcat:cxz3wkxu3vay3evl4jxvf3fwi4

Nanopore sequencing and its application to the study of microbial communities

Laura Ciuffreda, Héctor Rodríguez-Pérez, Carlos Flores
2021 Computational and Structural Biotechnology Journal  
Since its introduction, nanopore sequencing has enhanced our ability to study complex microbial samples through the possibility to sequence long reads in real time using inexpensive and portable technologies  ...  The use of long reads has allowed to address several previously unsolved issues in the field, such as the resolution of complex genomic structures, and facilitated the access to metagenome assembled genomes  ...  Given that long reads facilitate accessing repetitive elements and structural variants, nanopore sequencing has improved our capacity for de novo assembly of genomes, metagenomes, and plasmids, which in  ... 
doi:10.1016/j.csbj.2021.02.020 pmid:33815688 pmcid:PMC7985215 fatcat:5sb4whobgfgyrgnmmhcuhiab34

Computational methods for 16S metabarcoding studies using Nanopore sequencing data

Andres Santos, Ronny van Aerle, Leticia Barrientos, Jaime Martinez-Urtaza
2020 Computational and Structural Biotechnology Journal  
In particular, Oxford Nanopore Technologies (ONT) introduced nanopore sequencing which has become very popular among molecular ecologists.  ...  Assessment of bacterial diversity through sequencing of 16S ribosomal RNA (16S rRNA) genes has been an approach widely used in environmental microbiology, particularly since the advent of high-throughput  ...  Acknowledgements Andres Santos work was supported by the grants CONICYT-Doctorado Nacional-2017-21171392; Universidad de La Frontera CD-FRO1204; Network for Extreme Environments Research (NXR17-0003);  ... 
doi:10.1016/j.csbj.2020.01.005 pmid:32071706 pmcid:PMC7013242 fatcat:mpvkugddevd5hcpqmnpkqb2vhm

Nanopore Technology and Its Applications in Gene Sequencing

Bo Lin, Jianan Hui, Hongju Mao
2021 Biosensors  
By embedding a nano-scale hole in a thin membrane and measuring the electrochemical signal, nanopore technology can be used to investigate the nucleic acids and other biomacromolecules.  ...  Moreover, this review focuses on the applications using nanopore gene sequencing technology, including the diagnosis of cancer, detection of viruses and other microbes, and the assembly of genomes.  ...  Table 2 concludes the normal machine learning algorithms and deep learning networks that could be used to construct the training program.  ... 
doi:10.3390/bios11070214 pmid:34208844 fatcat:tcc43whzrbgtxjcqvlijihso3q

A sequencer coming of age: De novo genome assembly using MinION reads

Carlos de Lannoy, Dick de Ridder, Judith Risse
2017 F1000Research  
Nanopore technology provides a novel approach to DNA sequencing that yields long, label-free reads of constant quality.  ...  Acknowledgements Giovanni Maglia (University of Groningen, Groningen, The Netherlands) provided helpful advice related to the physical basis of nanopore sequencing.  ...  Currently, the most prominent obstacle for de novo sequencing using the MinION is the high error rate of the reads.  ... 
doi:10.12688/f1000research.12012.1 pmid:29375809 pmcid:PMC5770995 fatcat:7rr3mi6esrehfjg7f7sh3fhtca

Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

Haotian Teng, Minh Duc Cao, Michael B Hall, Tania Duarte, Sheng Wang, Lachlan J M Coin
2018 GigaScience  
Here, we report Chiron, the first deep learning model to achieve end-to-end basecalling and directly translate the raw signal to DNA sequence without the error-prone segmentation step.  ...  Chiron achieves basecalling speeds of more than 2,000 bases per second using desktop computer graphics processing units.  ...  [14] for the open Human nanopore dataset.  ... 
doi:10.1093/gigascience/giy037 pmid:29648610 pmcid:PMC5946831 fatcat:g5k6d7e3ijg7ln3qd6wn2aumbq
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