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181 results for “Nanopore sequencing”
NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy
<p>The data presented in "NanoGalaxy: A Galaxy tool kit with workflows for third-generation sequence analysis" to illustrate the functionality of the tools was obtained from: Wick, Ryan R., et al. "Completing bacterial genome assemblies with multiplex MinION sequencing." <em>Microbial genomics</em> 3.10 (2017).</p> <p>+</p> <p>Li, Ruichao, et al. "Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data." <em>Gigascience</em> 7.3 (2018): gix132.</p>
Data from: Chromosome-level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of Nanopore Sequencing, Bionano and Hi-C technology
<p><i>Onychostoma macrolepis</i> is an emerging commercial cyprinid fish species. It is a model system for studies of sexual dimorphism and genome evolution. Here, we report the chromosome-level assembly of the<i> O.macrolepis</i> genome obtained from the integration of Nanopore long-read sequencing with physical maps produced using Bionano and Hi-C technology. A total of 87.9 Gb of Nanopore sequence provided approximately 100-fold coverage of the genome. The preliminary genome assembly was 883.2 Mb in size with a contig N50 size of 11.2 Mb. The 969 corrected contigs obtained from Bionano optical mapping were assembled into 853 scaffolds and produced an assembly of 886.5 Mb with a scaffold N50 of 16.5 Mb. Finally, using the Hi-C data, 881.3 Mb (99.4% of genome) in 526 scaffolds were anchored and oriented in 25 chromosomes ranging in size from 25.27 to 56.49 Mb. In total, 24,770 protein-coding genes were predicted in the genome, and ~96.85% of the genes were functionally annotated. The annotated assembly contains 93.3% complete genes from the BUSCO reference set. In addition, we identified 409 Mb (46.23% of the genome) of repetitive sequence, and 11,213 non-coding RNAs, in the genome. Evolutionary analysis revealed that <i>O.macrolepis</i> diverged from common carp approximately 24.25 million years ago. The chromosomes of <i>O.macrolepis</i> showed an unambiguous correspondence to the chromosomes of zebrafish. The high-quality genome assembled in this work provides a valuable genomic resource for further biological and evolutionary studies of <i>O. macrolepis</i>.</p>
Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding
<p>Description of 1200bp amplicon primer sets and .bed and .tsv files for SARS-CoV-2 assembly using the ARTIC bioinformatics pipeline.</p>
Oxford Nanopore Direct RNA Sequencing datasets for detecting rRNA modifications in the Brassica oleracea mitoribosome
<p>Oxford Nanopore Direct RNA Sequencing (DRS) was applied for the detection of rRNA modifications in the <em>Brassica oleracea</em> mitoribosome. A comparison between native rRNA transcripts and in vitro transcribed (IVT) rRNA transcripts that were devoid of any modification indicated systematic base-calling errors and/or variations in current intensities that led to the prediction of the modified nucleotides (Begik et al., 2018).</p> <p>For Nanopore (DRS) library preparation, custom reverse transcription adapters (RTAs) containing Deeplexicon multiplexing barcodes (BC1, BC2 or BC3) were designed for sequence-specific ligation to the 3’-ends of <em>B. oleracea</em> mitochondrial rRNAs.</p> <p>Basecalling and demultiplexing of ONT direct RNA sequencing data were performed by Guppy and Deeplexicon, respectively.</p> <p>For the analysis and visualization of current intensities, a full description is available in the associated publication.</p> <p>The <strong>Eventalign_18S.R</strong> Rscript was used to make the nanopore <strong>18S </strong>signal analysis</p> <p>The <strong>Eventalign_26S.R</strong> Rscript was used to make the nanopore <strong>26S </strong>signal analysis</p> <p>The raw data for the scripts are in the following folders:</p> <p>- For 26S: 26S_Native.barcode01 and 26S_IVT.barcode03<br>- For 18S: 18S_Native.barcode01 and 18S_IVT.barcode02</p> <p>These folders contain the read alignment files output from minimap2 (in .bam format) and the eventalign files generated by the f5c software (in tsv format).</p> <p>The FASTA folder contains the mitochondrial 18S and 26S rRNA gene reference sequence in fasta format</p>
Using a mobile Nanopore sequencing lab for end-to-end genomic surveillance of Plasmodium falciparum: a feasibility study
Open the record for dataset details and reuse information.
Data from: Estimating bloodstain age in the short term based on DNA fragment length using nanopore sequencer
<p>We used a nanopore sequencer to quantify DNA fragments > 10,000 bp in size and then evaluated their relationship with short-term bloodstain age. Moreover, DNA degradation was investigated after bloodstains were wetted once with water. Bloodstain samples on cotton gauze were stored at room temperature and low humidity for up to 6 months. Bloodstains stored for 1 day were wetted with nuclease-free water, allowed to dry, and stored at room temperature and low humidity for up to 1 week. The proportion of fragments > 20,000 bp in dry bloodstains tended to decrease over time, particularly for fragments > 50,000 bp in size. This trend was modeled using a power approximation curve, with the highest R2 value (0.6475) noted for fragments > 50,000 bp in size; lower values were recorded for shorter fragments. The proportion of longer fragments was significantly reduced in bloodstains that were dried after being wetted once, and there was significant difference in fragments > 50,000 bp between dry conditions and once-wetted. This result suggests that even temporary exposure to water causes significant DNA fragmentation, but not extensive degradation. Thus, bloodstains that appear fresh but have a low proportion of long DNA fragments may have been wetted previously. Our results indicate that evaluating the proportion of long DNA fragments yields information on both bloodstain age and the environment in which they were stored.</p>
Matched Oxford Nanopore Technologies and Bisulfite Sequencing of the GM24385 Cell Line
<p>One of the most widespread genomic modifications is 5-methylcytosine (5mC), which most frequently occurs at <a href="https://en.wikipedia.org/wiki/CpG_site">CpG</a> dinucleotides. Compared to whole-genome bisulfite sequencing, the traditional method of 5mC detection, nanopore technology can offer many advantages such as simplicity of sample prep and subsequent analysis.</p> <p>In order to demonstrate the utility and convenience of Oxford Nanopore Technologies’ sequencing platform for performing detection and analysis of 5mC, we have sequenced the HG002 Genome in a Bottle Sample GM24385 with both traditional bisulfite sequencing and using nanopore sequencing. Both technologies, old and new, were applied to the same sample from a single DNA extraction.</p> <p><em>Bisulfite sequencing</em></p> <p>Bisulfite sequencing was performed by a commercial provider and processed with the commonly used <a href="https://www.bioinformatics.babraham.ac.uk/projects/bismark/">bismark</a> package to obtain the proportion of reads displaying methylation at CpG sites throughout the whole genome. </p> <p><em>Nanopore sequencing</em></p> <p>Nanopore sequencing was performed using the same sample of GM24385 material sent for bisulfite sequencing. Sequencing was performed on the MinION platform, across multiple flowcells, as part of ongoing platform development activities. The sequencing was not performed explicitly for the analysis presented here; we are making available all sequencing runs undertaken with this sample for the benefit of the community.</p> <p><em>Data Access</em></p> <p>Data is available as part of the Registry of Open Data on AWS: https://registry.opendata.aws/ont-open-data/. This dataset can be accessed through the S3 prefix:</p> <blockquote> <p>s3://ont-open-data/gm24385_mod_2021.09/</p> </blockquote> <p><em>Further Information</em></p> <ul> <li>https://labs.epi2me.io/gm24385-5mc/</li> <li>https://labs.epi2me.io/gm24385-5mc-remora</li> </ul>
Supplementary Information of Amplicon-based nanopore sequencing of patients with COVID-19 omicron (B.1.1.529) variant from India
<p><strong>We report sequencing of omicron variants from SARS-CoV-2 in 75 patients, using Nanopore long-read sequencing chemistry. We highlight the nature of mutations in spike glycoprotein that are unique and common to other populations.</strong></p> <p> </p>
Data for for Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing
<p>Datasets accompanying the paper https://doi.org/10.1101/2021.10.18.464684</p>
Data used in the study "Application of nanopore sequencing for accurate identification of bioaerosol-derived bacterial colonies"
<p>Data used in the study "Application of nanopore sequencing for accurate identification of bioaerosol-derived bacterial colonies." The datasets contain nanopore and Sanger sequencing data (including the electropherograms) as well as EPI2ME and NGSpeciesID analysis.</p>
Assessment of a multiplex PCR and Nanopore-based method for portable dengue virus sequencing in Indonesia
<p>Multiplex primer sets for amplification of the complete coding region of Indonesian dengue virus.</p>
Sequencing summary files for "Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples"
<p>Sequencing summary files for experiments in "Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples". </p>
Comprehensive benchmark and architectural analysis of deep learning models for Nanopore sequencing basecalling
<p>Placeholder data for the Lambda phage data used in: Comprehensive benchmark and architectural analysis of deep learning models for Nanopore sequencing basecalling.</p> <p>For the complete dataset see the Sequence Read Archive under the PRJNA926802 bioproject ID.</p>
Nanopore Sequencing of Double-Stranded RNA (dsRNA) for Plant Virus and Viroid Detection
<p>Thi file contain results of 24 grapevines leaf samples analyzed using dsRNA-MiSeq (Illumina Miseq) and dsRNAcD sequencing (ONT nanopore), that were used in the following article ''<strong>Nanopore Sequencing of Double-Stranded RNA (dsRNA) for Plant Virus and Viroid Detection'' </strong> submitted in Frontiers in Microbiology </p>
Peptide sequencing based on host-guest interaction-assisted nanopore sensing
<p>Source data files of "Peptide sequencing based on host-guest interaction-assisted nanopore sensing"</p>
Peptide sequencing based on host-guest interaction-assisted nanopore sensing
<p>Source data for "Peptide sequencing based on host-guest interaction-assisted nanopore sensing"</p>
De novo nanopore sequencing overrepresents RNA modification landscape, part 2
<p>RNA modifications are critical to the functional diversity and regulatory complexity of the transcriptome. With increasing frequency, direct nanopore RNA sequencing is applied to identify RNA modifications de novo. Here, we directly compare the MS2 phage genome RNA modification profiles determined using nanopore to orthogonal LC-MS/MS assays. The results reveal very different views of the modification landscape, suggesting caution when calling new RNA modifications using nanopore alone.</p>
De novo nanopore sequencing overrepresents RNA modification landscape, part 3
<p>RNA modifications are critical to the functional diversity and regulatory complexity of the transcriptome. With increasing frequency, direct nanopore RNA sequencing is applied to identify RNA modifications de novo. Here, we directly compare the MS2 phage genome RNA modification profiles determined using nanopore to orthogonal LC-MS/MS assays. The results reveal very different views of the modification landscape, suggesting caution when calling new RNA modifications using nanopore alone.</p>
Evaluation of a mNGS Workflow for Infection Diagnosis Using Oxford Nanopore Sequencing.
ClinicalTrials.gov study NCT04864873. IPD Sharing: NO. Countries: 1. Publications: 12.
Application of Nanopore Adaptive Sequencing
ClinicalTrials.gov study NCT06542042. IPD Sharing: NO. Countries: 1. Publications: 1.
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International Brain Laboratory public data
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OpenNeuro
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