Nanopore Technologies(纳米孔技术)研究综述
Nanopore Technologies 纳米孔技术 - Sequencing of long amplicons is one of the major benefits of Nanopore technologies, as it allows for reads much longer than Illumina. [1] This pattern recognition method has been differentiated from simple detection methods based on DNA self-assembly and nanopore technologies. [2] A mycoplasma strain was then isolated from a starling swab and its whole genome was sequenced using both Illumina and Nanopore technologies. [3] The genome of CA-230715 was sequenced using PacBio, Illumina, and Nanopore technologies. [4] Here, we sequenced the total DNA of Sacha inchi by using Illumina and Nanopore technologies and approached a de novo reconstruction of the whole nucleotide sequence and the organization of its 164,111 bp length of the chloroplast genome, displaying two copies of an inverted repeat sequence [inverted repeat A (IRA) and inverted repeat B (IRB)] of 28,209 bp, each one separating a small single copy (SSC) region of 17,860 bp and a large single copy (LSC) region of 89,833 bp. [5]长扩增子的测序是 Nanopore 技术的主要优势之一，因为它允许读取比 Illumina 更长的时间。 [1] 这种模式识别方法已区别于基于 DNA 自组装和纳米孔技术的简单检测方法。 [2] 然后从椋鸟拭子中分离出支原体菌株，并使用 Illumina 和 Nanopore 技术对其全基因组进行测序。 [3] 使用 PacBio、Illumina 和 Nanopore 技术对 CA-230715 的基因组进行了测序。 [4] 在这里，我们使用 Illumina 和 Nanopore 技术对 Sacha inchi 的总 DNA 进行了测序，并对整个核苷酸序列和叶绿体基因组 164,111 bp 长度的组织进行了从头重建，显示了两个反向重复序列副本 [inverted 28,209 bp 的重复 A (IRA) 和反向重复 B (IRB)]，每个分离一个 17,860 bp 的小单拷贝 (SSC) 区域和一个 89,833 bp 的大单拷贝 (LSC) 区域。 [5]
long read sequencing 长读测序
0) using Oxford Nanopore Technologies long-read sequencing to produce a chromosome-scale assembly. [1] Data description These data include raw sequences from four separate sequencing runs of the metagenome of a single individual of Halichondria panicea - one Illumina MiSeq (2×300 bp, paired-end) run and three Oxford Nanopore Technologies (ONT) long-read sequencing runs, generating 53. [2] To address this problem, we sequenced strain Lyd2019 from China using Oxford Nanopore Technologies (ONT) long-read sequencing and Illumina short-read sequencing. [3] In this article, we review and compare 2 prevailing long-read sequencing technologies, Pacific Biosciences and Oxford Nanopore Technologies, and discuss their applications in neurodegenerative diseases. [4] litchii strain ZL2018 from China using Oxford Nanopore Technologies (ONT) long-read sequencing and Illumina short-read sequencing. [5] Novel lncRNAs were validated with Oxford Nanopore Technologies long-read sequencing. [6] Results We have used Oxford Nanopore Technologies long-read sequencing to update and validate the quality and contiguity of the T. [7] Oxford Nanopore Technologies (ONT) offers the ability to generate long-read sequencing data in real time via portable protein nanopore USB devices. [8] Significant recent progress in long-read sequencing technologies such as PacBio and Oxford Nanopore Technologies (ONT) also brought about a large variety of assemblers. [9] The Oxford Nanopore Technologies long read sequencing by nanopores provides a portable and cost-efficient platform for sequencing assays opening the possibility of its application outside specialized environments and real-time analysis of data. [10] With the advantages that long-read sequencing platforms such as Pacific Biosciences (Menlo Park, CA, USA) (PacBio) and Oxford Nanopore Technologies (Oxford, UK) (ONT) can offer, various research fields such as genomics and transcriptomics can exploit their benefits. [11] Significant recent progress in long-read sequencing technologies such as PacBio and Oxford Nanopore Technologies (ONT) has also brought about a large variety of assemblers. [12] Background Long-read sequencing is revolutionizing genome assembly: as PacBio and Nanopore technologies become more accessible in technicity and in cost, long-read assemblers flourish and are starting to deliver chromosome-level assemblies. [13] This chromosomal-level assembly was generated using Illumina sequencing in conjunction with Oxford Nanopore Technologies long read sequencing and HiC chromatin conformation capture sequencing. [14] Long read sequencing approaches, such as Oxford Nanopore Technologies (ONT), have the ability to reduce time to results for the detection of uSVs with the same resolution of current state-of-the-art diagnostic tests. [15] This study proposes a comparison in SVs detection and characterization from long-read sequencing obtained with the MinION device developed by Oxford Nanopore Technologies and from optical mapping produced by the Saphyr device commercialized by Bionano Genomics. [16] We re-sequenced five Histoplasma strains (WU24 (NAm 1), G217B (NAm 2), H88 (African), G186AR (Panama), and G184AR (Panama)) using Oxford Nanopore Technologies long-read sequencing technology. [17] In this study, we used two long-read sequencing (LRS) techniques, Sequel from the Pacific Biosciences and MinION from Oxford Nanopore Technologies, for the transcriptional characterization of a prototype baculovirus, Autographacalifornica multiple nucleopolyhedrovirus. [18] Background The application of long-read sequencing using the Oxford Nanopore Technologies (ONT) MinION sequencer is getting more diverse in the medical field. [19] Application of Oxford Nanopore Technologies’ long-read sequencing platform to transcriptomic analysis is increasing in popularity. [20]0) 使用 Oxford Nanopore Technologies 长读长测序来产生染色体规模的组装。 [1] 数据描述 这些数据包括来自于四次单独的 Halichondria panicea 个体宏基因组测序运行的原始序列 - 一次 Illumina MiSeq（2×300 bp，双末端）运行和三个 Oxford Nanopore Technologies (ONT) 长读长测序运行，生成 53。 [2] nan [3] nan [4] nan [5] 使用 Oxford Nanopore Technologies 长读长测序验证了新型 lncRNA。 [6] nan [7] nan [8] nan [9] nan [10] nan [11] nan [12] nan [13] nan [14] nan [15] nan [16] nan [17] nan [18] nan [19] nan [20]
whole genome sequencing 全基因组测序
This study developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic-resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole-genome sequencing. [1] Viral whole genome sequencing was performed using Oxford Nanopore Technologies MinION platform. [2] We evaluated performance with a human whole-genome sequencing dataset and demonstrated that Halcyon outperformed existing third-party basecallers and achieved competitive performance against the latest Oxford Nanopore Technologies’ basecallers. [3] Our previous study demonstrated that whole genome sequencing (WGS) data generated by Oxford Nanopore Technologies (ONT) can be used for rapid and accurate prediction of selected Salmonella serotypes. [4] Motivation InterARTIC is an interactive web application for the analysis of viral whole-genome sequencing (WGS) data generated on Oxford Nanopore Technologies (ONT) devices. [5] enterocolitica clinical isolates during the Swedish outbreak using a combination of Illumina HiSeq short-read and Nanopore Technologies’ MinION long-read whole-genome sequencing. [6] The use of whole genome sequencing (WGS) data generated by the long-read sequencing platform Oxford Nanopore Technologies (ONT) has been shown to provide reliable results for Salmonella serotype prediction in a previous study. [7] Individual colonies were examined for blaNDM, and blaNDM-positive bacteria were characterized based on whole-genome sequencing (WGS) data from the Illumina and Oxford Nanopore Technologies (ONT) platforms. [8] The complete genomes of four Brachyspira hyodysenteriae isolates of the four different sequence types (STs) (ST6, ST66, ST196, and ST197) causing swine dysentery in Switzerland were generated by whole-genome sequencing and de novo hybrid assembly of reads obtained from second (Illumina) and third (Oxford Nanopore Technologies and Pacific Biosciences) high-throughput sequencing platforms. [9] We have developed two random primed SMART-Seq approaches, ‘SMART-9N’, and a version compatible with barcoded PCR primers available from Oxford Nanopore Technologies, ‘Rapid SMART-9N’, for the detection, characterization, and whole-genome sequencing of RNA viruses. [10] Based on several outbreaks diagnosed on commercial guinea flocks raised in France since 2017, we performed direct whole-genome sequencing from pancreatic lesional tissue by using the Oxford Nanopore Technologies (ONT) sequencing method. [11] Definition of SARS-CoV-2 variant was carried out by Sanger sequencing of relevant S-gene regions and, in some cases, by whole genome sequencing (WGS) using the ARTIC-nCoV workflow on a MiniION (Oxford Nanopore Technologies, Oxford, UK) or a MiSeq ILLUMINA platform (San Diego, California, US). [12] In this feasibility study, we demonstrate that whole genome sequencing of circulating cell-free DNA using conventional Oxford Nanopore Technologies (ONT) sequencing can accurately detect cell-of-origin and cancer-specific 5mC changes while preserving important fragmentomic information. [13]本研究基于牛津纳米孔技术 (ONT) DNA 全基因组测序，开发并验证了一套完整的分析方案，用于更快、更准确地监测和调查抗生素抗性微生物。 [1] 使用 Oxford Nanopore Technologies MinION 平台进行病毒全基因组测序。 [2] nan [3] nan [4] nan [5] nan [6] nan [7] nan [8] nan [9] nan [10] nan [11] nan [12] nan [13]
next generation sequencing 下一代测序
Here the Association of Biomolecular Resource Facilities (ABRF) Next-Generation Sequencing Study benchmarks the performance of a set of sequencing instruments (HiSeq/NovaSeq/paired-end 2 × 250-bp chemistry, Ion S5/Proton, PacBio circular consensus sequencing (CCS), Oxford Nanopore Technologies PromethION/MinION, BGISEQ-500/MGISEQ-2000 and GS111) on human and bacterial reference DNA samples. [1] Next-generation sequencing (NGS) has become the gold standard for advanced microbiome analysis; however, 3rd generation real-time sequencing, such as Oxford Nanopore Technologies (ONT), enables rapid sequencing from several kilobases to >2 Mb with high resolution. [2] The portable next-generation sequencing devices developed by Oxford Nanopore Technologies (ONT) are attractive alternatives due to their long-read sequence capability, compact low-cost hardware, and continued improvements in accuracy and throughput. [3] Summary In this study, six bacterial isolates with variable GC, including Escherichia coli as mesophilic reference strain, were selected to compare hybrid assembly strategies based on next-generation sequencing (NGS) of short reads, single-tube long-fragment reads (stLFR) sequencing, and Oxford Nanopore Technologies (ONT) sequencing platforms. [4] The new next-generation sequencing platforms by Oxford Nanopore Technologies for direct RNA sequencing (direct RNA-seq) allow for an in-depth and comprehensive study of the epitranscriptome by enabling direct base calling of RNA modifications. [5]在这里，生物分子资源设施协会 (ABRF) 下一代测序研究对一组测序仪器（HiSeq/NovaSeq/paired-end 2 × 250-bp 化学、Ion S5/Proton、PacBio 循环共有测序（CCS )、Oxford Nanopore Technologies PromethION/MinION、BGISEQ-500/MGISEQ-2000 和 GS111) 用于人类和细菌参考 DNA 样本。 [1] 新一代测序 (NGS) 已成为高级微生物组分析的黄金标准；然而，第三代实时测序，例如 Oxford Nanopore Technologies (ONT)，可以实现从几千碱基到 >2 Mb 的高分辨率快速测序。 [2] nan [3] nan [4] nan [5]
short read sequencing 短读测序
flavus NRRL 3357 genome, accomplished via long-read PacBio and Oxford Nanopore technologies combined with Illumina short-read sequencing. [1] lactis BB-12 was sequenced using Oxford Nanopore Technologies long-read and Illumina short-read sequencing platforms. [2] In this study, we carried out a systematic analysis on the pseudorabies virus transcriptome by combining our current data obtained by using Pacific Biosciences Sequel and Oxford Nanopore Technologies MinION sequencing with our earlier data generated by other LRS and short-read sequencing techniques. [3] Herein, short-read sequencing approaches are represented by the most prevalent technologies, Illumina and Ion Torrent, and long-read sequencing approaches are represented by Pacific Biosciences and Oxford Nanopore technologies. [4]flavus NRRL 3357 基因组，通过长读长 PacBio 和 Oxford Nanopore 技术结合 Illumina 短读长测序完成。 [1] lactis BB-12 使用 Oxford Nanopore Technologies 长读长和 Illumina 短读长测序平台进行测序。 [2] nan [3] nan [4]
single molecule sequencing 单分子测序
Owing to the complex nature of HLA genes and consequent challenges in allele assignment, Oxford Nanopore Technologies’ (ONT) single-molecule sequencing technology has been of great interest due to its fitness for sequencing long reads. [1] Recently, the single-molecule sequencing techniques such as the direct RNA sequencing platform offered by Oxford Nanopore technologies enable direct detection of RNA modifications on the molecule that is being sequenced, but to our knowledge this technology has not been used to identify RNA Pseudouridine sites. [2] Recently, sequencing of full-length transcripts based on the single-molecule sequencing platform from Oxford Nanopore Technologies (ONT) was introduced and is widely employed to sequence eukaryotic and viral RNAs. [3]由于 HLA 基因的复杂性以及随之而来的等位基因分配挑战，Oxford Nanopore Technologies (ONT) 的单分子测序技术因其适用于长读长测序而备受关注。 [1] 最近，牛津纳米孔技术提供的单分子测序技术（如直接 RNA 测序平台）能够直接检测正在测序的分子上的 RNA 修饰，但据我们所知，该技术尚未用于鉴定 RNA 假尿苷位点。 [2] nan [3]
high throughput sequencing 高通量测序
The data of high-throughput sequencing are provided as Excel spreadsheets, where the data on FPKM and TMP values were evaluated for the whole transcriptome with both Illumina HiSeq and Oxford Nanopore Technologies MinION sequencing. [1] nicotianae BL162 (P6303 WPC) (3984 contigs for 108 Mb) generated with MinION long-read High-Throughput Sequencing (HTS) technology (Oxford Nanopore Technologies, ONT). [2] Here we explored the intra-genomic diversity of Nassellaria and Spumellaria specimens (Radiolaria) by comparing Sanger sequencing with two different high-throughput sequencing platforms: Illumina and Oxford Nanopore Technologies (MinION). [3]高通量测序数据以 Excel 电子表格的形式提供，其中 FPKM 和 TMP 值的数据通过 Illumina HiSeq 和 Oxford Nanopore Technologies MinION 测序对整个转录组进行了评估。 [1] 使用 MinION 长读长高通量测序 (HTS) 技术 (Oxford Nanopore Technologies, ONT) 生成的烟草 BL162 (P6303 WPC) (3984 contigs for 108 Mb)。 [2] nan [3]
Oxford Nanopore Technologies 牛津纳米孔技术
We sequenced four bla CTX-M-27-positive MSM Shigella isolates (2018-20) using Oxford Nanopore Technologies; three S. [1] We sequenced both the DNA and RNA of this species using both the Oxford Nanopore Technologies and Illumina platforms. [2] Oxford Nanopore Technologies (ONT) sequencing platforms currently offer two approaches to whole-genome native-DNA library preparation: ligation and rapid. [3] Background Oxford Nanopore Technologies’ instruments can sequence reads of great length. [4] monocytogenes and at the same time the generation of genetic information that enables an estimation regarding the strain diversity in a sample, quasimetagenomic sequencing was performed early during enrichment in the presence of the background microbiota using Oxford Nanopore Technologies Flongle and Illumina MiSeq sequencing. [5] The MinION platform from Oxford Nanopore Technologies performs sequencing by passing single-strands of DNA through a layer of biological nanopore sensors; although sequencing is performed on single-strands, the recommended template by the manufacturer is double-stranded. [6] With the introduction of native RNA sequencing by Oxford Nanopore Technologies, it is now possible to sequence full-length native RNA. [7] Here we show how the real-time nature of Oxford Nanopore Technologies sequencers can accelerate consensus generation, lineage and variant status assignment. [8] pharaonis using a long-read platform (Oxford Nanopore Technologies PromethION) to assemble the genome and short-read, high quality technology (Illumina HiSeq X Ten) to correct for sequencing errors. [9] Methods We conducted Oxford Nanopore Technologies (Oxford, United Kingdom (UK)) metagenomic sequencing for 180 respiratory samples from a UK hospital during the 2018/19 influenza season, and compared results to routine molecular diagnostic standards (Xpert Xpress Flu/RSV assay; BioFire FilmArray Respiratory Panel 2 assay). [10] 5 kbp with a quality enabling variant-calling by using a portable sequencer (MinION, Oxford Nanopore Technologies). [11] Oxford Nanopore Technologies (ONT) sequencing offers a promising, cost-effective approach to the sequencing of long amplicons such as near full-length HIV-1 proviruses, but the high diversity of HIV-1 and the ONT sequencing error render analysis of the generated data difficult. [12] Findings We applied a combination of Illumina sequencing, Oxford Nanopore Technologies sequencing, and high-throughput chromosome conformation capture technologies to construct a chromosome-level genome of the hard-shelled mussel, with a total length of 1. [13] To achieve high-quality genome assemblies, we used Oxford Nanopore Technologies and Illumina platforms. [14] Infectious disease monitoring on Oxford Nanopore Technologies (ONT) platforms offers rapid turnaround times and low cost, exemplified by well over a half of million ONT SARS-COV-2 datasets. [15] Owing to the complex nature of HLA genes and consequent challenges in allele assignment, Oxford Nanopore Technologies’ (ONT) single-molecule sequencing technology has been of great interest due to its fitness for sequencing long reads. [16] INSaFLU-TELE-Vir handles NGS data collected from distinct sequencing technologies (Illumina, Ion Torrent and Oxford Nanopore Technologies), with the possibility of constructing comparative analyses using different technologies. [17] Here, we performed transcriptome sequencing using the Oxford Nanopore Technologies (ONT) MinION platform for asparagus (Asparagus officinalis L. [18] With Cas9-guided RNPs to specifically target the HBV genome, we enriched in HBV DNA from primary human hepatocytes (PHHs) infected with different HBV genotypes, as well as enriching in HBV from infected patient liver tissue, followed by sequencing with Oxford Nanopore Technologies MinION. [19] To fill this gap, we optimized the Oxford Nanopore Technologies’ sequencing protocol, obtaining sequencing reads with an N50 of 62 kb—a very high value for a plant sample. [20] One particular technology is the nanopore-based sequencer, MinION, developed by Oxford Nanopore Technologies (ONT). [21] Oxford Nanopore Technologies’ (ONT) long read sequencers offer access to longer DNA fragments than previous sequencer generations, at the cost of a higher error rate. [22] Using Cas9 endonuclease activity, segments of the complex KIR gene cluster were enriched and sequenced on an Oxford Nanopore Technologies platform. [23] The genome assembly was generated by combining short-read Illumina HiSeq-X Ten and long-read Oxford Nanopore Technologies MinION sequence data using the Unicycler assembler. [24] We sequenced both the DNA and RNA of this species using both the Oxford Nanopore Technologies (ONT) and Illumina platforms. [25] The data of high-throughput sequencing are provided as Excel spreadsheets, where the data on FPKM and TMP values were evaluated for the whole transcriptome with both Illumina HiSeq and Oxford Nanopore Technologies MinION sequencing. [26] Here, we report an innovative approach using Oxford Nanopore Technologies (ONT)-based amplicon sequencing. [27] Here we present a de novo genome assembly and structural annotation for the coconut rhinoceros beetle, Oryctes rhinoceros (Coleoptera: Scarabaeidae), based on Oxford Nanopore Technologies (ONT) long-read data generated from a wild-caught female, as well as the assembly process that also led to the recovery of the complete circular genome assemblies of the beetle’s mitochondrial genome and that of the biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). [28] 0) using Oxford Nanopore Technologies long-read sequencing to produce a chromosome-scale assembly. [29] Viral genomes were then sequenced on either an Illumina MiSeq or an Oxford Nanopore Technologies (ONT) GridION. [30] Toward this end, we compared the results obtained from different transcriptome analysis platforms (quantitative polymerase chain reaction, Illumina RNASeq, and Oxford Nanopore Technologies MinION) for the transcriptome encoded by human chromosome 18 (Chr 18) using the same sample types (HepG2 cells and liver tissue). [31] This study developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic-resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole-genome sequencing. [32] Viral whole genome sequencing was performed using Oxford Nanopore Technologies MinION platform. [33] SARS-CoV-2 genome sequencing was performed using Oxford Nanopore Technologies MinION, following the ARTIC Network protocols. [34] The Oxford Nanopore Technologies (ONT) MinION™ is an affordable and small footprint DNA sequencing device with the potential to quickly deliver reliable and cost effective data. [35] Sequencing was performed in a hand-held Oxford Nanopore Technologies MinION sequencer. [36] Data description These data include raw sequences from four separate sequencing runs of the metagenome of a single individual of Halichondria panicea - one Illumina MiSeq (2×300 bp, paired-end) run and three Oxford Nanopore Technologies (ONT) long-read sequencing runs, generating 53. [37] Oxford Nanopore Technologies (ONT) sequencing was performed in C. [38] We evaluated performance with a human whole-genome sequencing dataset and demonstrated that Halcyon outperformed existing third-party basecallers and achieved competitive performance against the latest Oxford Nanopore Technologies’ basecallers. [39] While Illumina sequencing platforms are most typically used, newer portable platforms, such as the Oxford Nanopore Technologies (ONT) MinION, offer the potential for rapid analysis of food chain microbiomes. [40] Here the Association of Biomolecular Resource Facilities (ABRF) Next-Generation Sequencing Study benchmarks the performance of a set of sequencing instruments (HiSeq/NovaSeq/paired-end 2 × 250-bp chemistry, Ion S5/Proton, PacBio circular consensus sequencing (CCS), Oxford Nanopore Technologies PromethION/MinION, BGISEQ-500/MGISEQ-2000 and GS111) on human and bacterial reference DNA samples. [41] To advance our understanding of the ovulation differences in Muscovy duck, we utilized the Oxford Nanopore Technologies (ONT) to generate transcriptome data from 3 groups of female duck ovaries with ovulation differences (i. [42] Here, we report draft genome sequences for eight Streptomyces strains that were isolated from multiple sky islands in Arizona and sequenced using an Oxford Nanopore Technologies Flongle adapter and MinION system. [43] In our study we present an overview of the use of Oxford Nanopore Technologies (ONT) sequencing technology on the background of Enteric fever. [44] Using this protocol, we have been successfully sequencing various fungi with a MinION (Oxford Nanopore Technologies). [45] To address this problem, we sequenced strain Lyd2019 from China using Oxford Nanopore Technologies (ONT) long-read sequencing and Illumina short-read sequencing. [46] Recently, the single-molecule sequencing techniques such as the direct RNA sequencing platform offered by Oxford Nanopore technologies enable direct detection of RNA modifications on the molecule that is being sequenced, but to our knowledge this technology has not been used to identify RNA Pseudouridine sites. [47] Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. [48] flavus NRRL 3357 genome, accomplished via long-read PacBio and Oxford Nanopore technologies combined with Illumina short-read sequencing. [49] Here, we apply deep (>50×) long-read Oxford Nanopore Technologies (ONT) sequencing to HEK293T cells infected with SARS-CoV-2, and do not find the virus integrated into the genome. [50]我们使用 Oxford Nanopore Technologies 对四个 bla CTX-M-27 阳性 MSM 志贺氏菌分离株（2018-20）进行了测序；三个S。 [1] 我们使用 Oxford Nanopore Technologies 和 Illumina 平台对该物种的 DNA 和 RNA 进行了测序。 [2] nan [3] nan [4] 单核细胞增多症，同时产生能够估计样品中菌株多样性的遗传信息，准宏基因组测序是在富集的早期使用 Oxford Nanopore Technologies Flongle 和 Illumina MiSeq 测序在存在背景微生物群的情况下进行的。 [5] nan [6] nan [7] nan [8] pharaonis 使用长读长平台 (Oxford Nanopore Technologies PromethION) 组装基因组，并使用短读长、高质量技术 (Illumina HiSeq X Ten) 来纠正测序错误。 [9] nan [10] nan [11] nan [12] 结果 我们结合 Illumina 测序、Oxford Nanopore Technologies 测序和高通量染色体构象捕获技术构建了硬壳贻贝的染色体水平基因组，总长度为 1。 [13] nan [14] nan [15] 由于 HLA 基因的复杂性以及随之而来的等位基因分配挑战，Oxford Nanopore Technologies (ONT) 的单分子测序技术因其适用于长读长测序而备受关注。 [16] nan [17] nan [18] 使用 Cas9 引导的 RNP 特异性靶向 HBV 基因组，我们从感染不同 HBV 基因型的原代人类肝细胞 (PHH) 中富集 HBV DNA，并从受感染的患者肝组织中富集 HBV，然后使用 Oxford Nanopore Technologies MinION 进行测序. [19] nan [20] nan [21] nan [22] 利用 Cas9 核酸内切酶活性，在 Oxford Nanopore Technologies 平台上对复杂 KIR 基因簇的片段进行富集和测序。 [23] 基因组组装是通过使用 Unicycler 组装器结合短读长 Illumina HiSeq-X Ten 和长读长 Oxford Nanopore Technologies MinION 序列数据生成的。 [24] nan [25] 高通量测序数据以 Excel 电子表格的形式提供，其中 FPKM 和 TMP 值的数据通过 Illumina HiSeq 和 Oxford Nanopore Technologies MinION 测序对整个转录组进行了评估。 [26] nan [27] nan [28] 0) 使用 Oxford Nanopore Technologies 长读长测序来产生染色体规模的组装。 [29] nan [30] nan [31] 本研究基于牛津纳米孔技术 (ONT) DNA 全基因组测序，开发并验证了一套完整的分析方案，用于更快、更准确地监测和调查抗生素抗性微生物。 [32] 使用 Oxford Nanopore Technologies MinION 平台进行病毒全基因组测序。 [33] nan [34] nan [35] nan [36] 数据描述 这些数据包括来自于四次单独的 Halichondria panicea 个体宏基因组测序运行的原始序列 - 一次 Illumina MiSeq（2×300 bp，双末端）运行和三个 Oxford Nanopore Technologies (ONT) 长读长测序运行，生成 53。 [37] nan [38] nan [39] nan [40] 在这里，生物分子资源设施协会 (ABRF) 下一代测序研究对一组测序仪器（HiSeq/NovaSeq/paired-end 2 × 250-bp 化学、Ion S5/Proton、PacBio 循环共有测序（CCS )、Oxford Nanopore Technologies PromethION/MinION、BGISEQ-500/MGISEQ-2000 和 GS111) 用于人类和细菌参考 DNA 样本。 [41] nan [42] 在这里，我们报告了从亚利桑那州的多个天空岛分离并使用 Oxford Nanopore Technologies Flongle 适配器和 MinION 系统进行测序的八种链霉菌菌株的基因组序列草图。 [43] nan [44] nan [45] nan [46] 最近，牛津纳米孔技术提供的单分子测序技术（如直接 RNA 测序平台）能够直接检测正在测序的分子上的 RNA 修饰，但据我们所知，该技术尚未用于鉴定 RNA 假尿苷位点。 [47] nan [48] flavus NRRL 3357 基因组，通过长读长 PacBio 和 Oxford Nanopore 技术结合 Illumina 短读长测序完成。 [49] nan [50]
nanopore technologies minion 纳米孔技术小黄人
With Cas9-guided RNPs to specifically target the HBV genome, we enriched in HBV DNA from primary human hepatocytes (PHHs) infected with different HBV genotypes, as well as enriching in HBV from infected patient liver tissue, followed by sequencing with Oxford Nanopore Technologies MinION. [1] The genome assembly was generated by combining short-read Illumina HiSeq-X Ten and long-read Oxford Nanopore Technologies MinION sequence data using the Unicycler assembler. [2] The data of high-throughput sequencing are provided as Excel spreadsheets, where the data on FPKM and TMP values were evaluated for the whole transcriptome with both Illumina HiSeq and Oxford Nanopore Technologies MinION sequencing. [3] Toward this end, we compared the results obtained from different transcriptome analysis platforms (quantitative polymerase chain reaction, Illumina RNASeq, and Oxford Nanopore Technologies MinION) for the transcriptome encoded by human chromosome 18 (Chr 18) using the same sample types (HepG2 cells and liver tissue). [4] Viral whole genome sequencing was performed using Oxford Nanopore Technologies MinION platform. [5] SARS-CoV-2 genome sequencing was performed using Oxford Nanopore Technologies MinION, following the ARTIC Network protocols. [6] Sequencing was performed in a hand-held Oxford Nanopore Technologies MinION sequencer. [7] In Phase 1, we will evaluate Oxford Nanopore Technologies MinION sequencing direct from blood in 50 blood culture-proven sepsis patients recruited from consecutive patients with suspected sepsis. [8] Viral genome sequencing was performed using Oxford Nanopore Technologies MinION platform. [9] In this study, we carried out a systematic analysis on the pseudorabies virus transcriptome by combining our current data obtained by using Pacific Biosciences Sequel and Oxford Nanopore Technologies MinION sequencing with our earlier data generated by other LRS and short-read sequencing techniques. [10] Here, we report on the complete, circular genome sequence obtained using Illumina MiSeq and Oxford Nanopore Technologies MinION reads in order to better resolve the phylogeny of a rare pathogen. [11] fusiformis genome was sequenced using Oxford Nanopore Technologies MinION and assembled using only ultra-long reads (>35 kb). [12]使用 Cas9 引导的 RNP 特异性靶向 HBV 基因组，我们从感染不同 HBV 基因型的原代人类肝细胞 (PHH) 中富集 HBV DNA，并从受感染的患者肝组织中富集 HBV，然后使用 Oxford Nanopore Technologies MinION 进行测序. [1] 基因组组装是通过使用 Unicycler 组装器结合短读长 Illumina HiSeq-X Ten 和长读长 Oxford Nanopore Technologies MinION 序列数据生成的。 [2] 高通量测序数据以 Excel 电子表格的形式提供，其中 FPKM 和 TMP 值的数据通过 Illumina HiSeq 和 Oxford Nanopore Technologies MinION 测序对整个转录组进行了评估。 [3] nan [4] 使用 Oxford Nanopore Technologies MinION 平台进行病毒全基因组测序。 [5] nan [6] nan [7] nan [8] nan [9] nan [10] nan [11] nan [12]
nanopore technologies long 纳米孔技术长
0) using Oxford Nanopore Technologies long-read sequencing to produce a chromosome-scale assembly. [1] Novel lncRNAs were validated with Oxford Nanopore Technologies long-read sequencing. [2] Results We have used Oxford Nanopore Technologies long-read sequencing to update and validate the quality and contiguity of the T. [3] The Oxford Nanopore Technologies long read sequencing by nanopores provides a portable and cost-efficient platform for sequencing assays opening the possibility of its application outside specialized environments and real-time analysis of data. [4] lactis BB-12 was sequenced using Oxford Nanopore Technologies long-read and Illumina short-read sequencing platforms. [5] This chromosomal-level assembly was generated using Illumina sequencing in conjunction with Oxford Nanopore Technologies long read sequencing and HiC chromatin conformation capture sequencing. [6] Twenty-five carbapenem-nonsusceptible isolates from a medical institution in Hanoi were sequenced on Illumina short-read sequencers, and 13 blaNDM-positive isolates, including isolates of Klebsiella pneumoniae, Escherichia coli, Citrobacter freundii, Morganella morganii, and Proteus mirabilis, were further sequenced on an Oxford Nanopore Technologies long-read sequencer to obtain complete plasmid sequences. [7] We re-sequenced five Histoplasma strains (WU24 (NAm 1), G217B (NAm 2), H88 (African), G186AR (Panama), and G184AR (Panama)) using Oxford Nanopore Technologies long-read sequencing technology. [8]0) 使用 Oxford Nanopore Technologies 长读长测序来产生染色体规模的组装。 [1] 使用 Oxford Nanopore Technologies 长读长测序验证了新型 lncRNA。 [2] nan [3] nan [4] lactis BB-12 使用 Oxford Nanopore Technologies 长读长和 Illumina 短读长测序平台进行测序。 [5] nan [6] nan [7] nan [8]
nanopore technologies sequencing 纳米孔技术测序
Findings We applied a combination of Illumina sequencing, Oxford Nanopore Technologies sequencing, and high-throughput chromosome conformation capture technologies to construct a chromosome-level genome of the hard-shelled mussel, with a total length of 1. [1] Here, we utilise Oxford Nanopore Technologies sequencing to produce a custom annotation of a well-studied human neuroblastoma cell line and to characterise isoform expression and usage across differentiation. [2] Genomes were completed using a hybrid assembly of Illumina and Oxford Nanopore Technologies sequencing reads and characterisation of the genetic context of resistance genes, multi-locus sequence types (STs) and phylogenetic analysis was determined bioinformatically. [3] Oxford Nanopore Technologies sequencing provided a complete genome sequence of P. [4] Oxford Nanopore Technologies sequencing, SEM-EDS imaging and chemical mapping were used to document the fungal and bacterial communities associated with the corrosion of the iron nails. [5] Motivation Oxford Nanopore Technologies sequencing devices support adaptive sequencing, in which undesired reads can be ejected from a pore in real time. [6] Furthermore, a neural network architecture designed to classify raw current signals generated by Oxford Nanopore Technologies sequencing ensures an average accuracy exceeding 60%, which is 39 times higher than that of random guessing. [7]结果 我们结合 Illumina 测序、Oxford Nanopore Technologies 测序和高通量染色体构象捕获技术构建了硬壳贻贝的染色体水平基因组，总长度为 1。 [1] 在这里，我们利用 Oxford Nanopore Technologies 测序对经过充分研究的人类神经母细胞瘤细胞系进行定制注释，并表征跨分化的异构体表达和使用。 [2] nan [3] nan [4] nan [5] nan [6] nan [7]
nanopore technologies platform 纳米孔技术平台
Using Cas9 endonuclease activity, segments of the complex KIR gene cluster were enriched and sequenced on an Oxford Nanopore Technologies platform. [1] Using Cas9 endonuclease activity, segments of the KIR gene cluster were enriched and sequenced on an Oxford Nanopore Technologies platform. [2] The LRGASP organizers have generated cDNA and direct RNA datasets in human, mouse, and manatee samples using different protocols followed by sequencing on Illumina, Pacific Biosciences, and Oxford Nanopore Technologies platforms. [3] In this paper, we present a large human long-read RNA-seq dataset using the Oxford Nanopore Technologies platform from 88 samples from GTEx tissues and cell lines, complementing the GTEx resource. [4] Here, using a combination of Illumina and Oxford Nanopore Technologies platforms, we produced a draft genome assembly of M. [5]利用 Cas9 核酸内切酶活性，在 Oxford Nanopore Technologies 平台上对复杂 KIR 基因簇的片段进行富集和测序。 [1] 利用 Cas9 核酸内切酶活性，KIR 基因簇的片段在 Oxford Nanopore Technologies 平台上进行富集和测序。 [2] nan [3] nan [4] nan [5]
nanopore technologies flongle 纳米孔技术 Flongle
monocytogenes and at the same time the generation of genetic information that enables an estimation regarding the strain diversity in a sample, quasimetagenomic sequencing was performed early during enrichment in the presence of the background microbiota using Oxford Nanopore Technologies Flongle and Illumina MiSeq sequencing. [1] Here, we report draft genome sequences for eight Streptomyces strains that were isolated from multiple sky islands in Arizona and sequenced using an Oxford Nanopore Technologies Flongle adapter and MinION system. [2] We demonstrate library preparation for Oxford Nanopore Technologies Flongle sequencing of low input DNA from individual juveniles and immature females, multiplexing up to twelve samples per flow cell. [3]单核细胞增多症，同时产生能够估计样品中菌株多样性的遗传信息，准宏基因组测序是在富集的早期使用 Oxford Nanopore Technologies Flongle 和 Illumina MiSeq 测序在存在背景微生物群的情况下进行的。 [1] 在这里，我们报告了从亚利桑那州的多个天空岛分离并使用 Oxford Nanopore Technologies Flongle 适配器和 MinION 系统进行测序的八种链霉菌菌株的基因组序列草图。 [2] nan [3]
nanopore technologies promethion 纳米孔技术 Promethion
pharaonis using a long-read platform (Oxford Nanopore Technologies PromethION) to assemble the genome and short-read, high quality technology (Illumina HiSeq X Ten) to correct for sequencing errors. [1] Here the Association of Biomolecular Resource Facilities (ABRF) Next-Generation Sequencing Study benchmarks the performance of a set of sequencing instruments (HiSeq/NovaSeq/paired-end 2 × 250-bp chemistry, Ion S5/Proton, PacBio circular consensus sequencing (CCS), Oxford Nanopore Technologies PromethION/MinION, BGISEQ-500/MGISEQ-2000 and GS111) on human and bacterial reference DNA samples. [2] Recent advances in throughput and accuracy mean that the Oxford Nanopore Technologies PromethION platform is a now a viable solution for genome sequencing. [3]pharaonis 使用长读长平台 (Oxford Nanopore Technologies PromethION) 组装基因组，并使用短读长、高质量技术 (Illumina HiSeq X Ten) 来纠正测序错误。 [1] 在这里，生物分子资源设施协会 (ABRF) 下一代测序研究对一组测序仪器（HiSeq/NovaSeq/paired-end 2 × 250-bp 化学、Ion S5/Proton、PacBio 循环共有测序（CCS )、Oxford Nanopore Technologies PromethION/MinION、BGISEQ-500/MGISEQ-2000 和 GS111) 用于人类和细菌参考 DNA 样本。 [2] nan [3]
nanopore technologies read 纳米孔技术 阅读
We also show how sequencing biases in both PacBio HiFi and Oxford Nanopore Technologies reads cause signature assembly errors that can be corrected with a diverse panel of sequencing technologies. [1] We also show how sequencing biases in both PacBio HiFi and Oxford Nanopore Technologies reads cause signature assembly errors that can be corrected with a diverse panel of sequencing technologies. [2]我们还展示了 PacBio HiFi 和 Oxford Nanopore Technologies 读取中的测序偏差如何导致签名组装错误，这些错误可以通过多种测序技术进行纠正。 [1] 我们还展示了 PacBio HiFi 和 Oxford Nanopore Technologies 读取中的测序偏差如何导致签名组装错误，这些错误可以通过多种测序技术进行纠正。 [2]