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175 results for “Long read sequencing”
Simulated eukaryotic genomic sequencing, long and short reads
<p><span>As accuracy and throughput of nanopore sequencing improves, it is increasingly common to perform long-read-first </span><em>de novo</em> genome assemblies followed by polishing with accurate short reads (Kim et al. 2021). We briefly introduce FMLRC2, the successor to the original FM-index Long Read Corrector (FMLRC), and illustrate its performance as a fast and accurate <em>de novo</em> assembly polisher for both bacterial and eukaryotic genomes.</p>
The data used in correspondence on the article entitled "Reply: Correspondence on NanoVar's performance outlined by Jiang T. et al. in 'Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation'."
<p>The data used in correspondence on the article entitled “Reply: Correspondence on NanoVar’s performance outlined by Jiang T. et al. in ‘Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation’.”. It contains the benchmarking results evaluated by Truvari. The running log files of NanoVar are also included in this repository.</p>
Purification of High Molecular Weight DNA for Long-Read Sequencing Using a High-Salt Gel Electroelution Trap
<p><strong>Figure 3. Yield and purity of HMW DNA obtained from difficult samples using the method proposed in this study</strong>.</p> <p>(A) The proposed method extracts more HMW DNA from a complex soil sample than a commercial column purification kit. Shown is a negative image of an ethidium bromide-stained agarose gel. Lane 1: 1/10 aliquot of ~90 ng of HMW DNA isolated using the E.Z.N.A. soil DNA extraction kit from a soil sample containing ~1,5 μg of total DNA (HMW DNA yield around 6%). Lane 2: ~100 ng of CTAB-extracted DNA from the same soil sample. ~10 μg of this crude DNA preparation was used as input for HMW DNA purification using the proposed method. Lane 3: 1/100 aliquot of ~3 μg of HMW DNA isolated using the proposed method from ~10 μg of the CTAB-extracted DNA (HMW DNA yield around 30%).</p> <p>(B) The proposed method yields high-purity HMW DNA from a complex plant sample, as determined by agarose gel electrophoresis. Lane 1: molecular weight marker (GeneRuler DNA ladder, Thermo Fisher Scientific). Lane 2: crude nucleic acid preparation extracted with SDS/Proteinase K from <em>Zingeria trichopoda</em> leaves, which served as an input for HMW DNA purification using the proposed method. Lane 3: purified HMW DNA. Note the absence of low-molecular-weight nucleic acids and heavy covalent complexes in the purified sample.</p> <p>(C) Same as (B) except that crude, CTAB-extracted DNA from a complex soil sample was used as an input for HMW DNA purification. Note the absence of a continuous smear of fragmented DNA as well as heavy covalent complexes in the purified sample (lane 3). Molecular weight marker sizes are indicated in base pairs to the left of each panel.</p>
Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data
<p>Source data for the paper "Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data"</p>
Simulated eukaryotic genomic sequencing, long and short reads
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Data from: Structural variation and its potential impact on genome instability: novel discoveries in the EGFR landscape by long-read sequencing
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Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning
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Data from: Haplotype sequence collection of ABO blood group alleles by long-read sequencing reveals putative A1-diagnostic variants
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Improved contiguity of the threespine stickleback genome using long-read sequencing
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Systematic profiling of full-length immunoglobulin and T-cell receptor repertoire diversity in rhesus macaque through long read transcriptome sequencing
<p>Using long read sequencing, we sequenced four Indian-origin rhesus macaque tissues. From raw full-length, non-chimeric circular consensus sequencing (CCS) reads, we obtained high quality, full-length sequences for over 6,000 unique immunoglobulin and T-cell receptor transcripts, without the need for sequence assembly.</p>
Consortium of Long Read Sequencing Database (CoLoRSdb)
<p>Visit the <a href="https://colorsdb.org">CoLoRSdb website</a> for additional information.</p>
Healthy and cancer individuals from Long-read sequencing reveals aberrant fragmentation patterns and origins of circulating DNA in cancer
<p>Oxford Nanopore sequencing data from 61 samples described in manuscript "Long-read sequencing reveals aberrant fragmentation patterns and origins of circulating DNA in cancer"<br><br></p> <p>All data are aligned to UCSC analysisSet hg38 (https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/), and use 0-based coordinates.</p> <p><strong>Level 2:</strong> In order to provide combined fragmentation and methylation information, Biscuit was used to create “epiBED” files (see Methods). epiBED files contain each read on a separate line, with each DNA methylation call on the read. epiBED files can be used for combined methylation/fragmentomic analysis, and are compatible with the CelFiE-ISH software that was used for cell of origin deconvolution.</p> <p>Creation of Biscuit EpiBED files:<br>Biscuit (https://huishenlab.github.io/biscuit/) v. 1.4.1-dev was used with the command “biscuit epiread -M -b 0 -m 0 -a 0 -5 0 -3 0 -y 0.9 -L 1000000 hg38.analysisSet.fa”, where the reference is the same UCSC reference genome used for alignment. Files are available in the Zenodo repository listed in Data Availability.</p> <p><strong>Level 3</strong>: DNA methylation BED files. BED files created by modkit (see Methods) provide one line for each CpG covered, and can be used for basic DNA methylation analysis.<br><br>Creation of modkit BED files:<br>BED files were created using modkit (https://github.com/nanoporetech/modkit) v. 0.1.5 with the command “modkit pileup --cpg --combine-strands --ignore h --filter-threshold 0.9 --bedgraph". </p> <p> </p>
Seq2scFv: a toolkit for the comprehensive analysis of display libraries from long-read sequencing platforms
<p>Annotation of full-length scFvs sequenced with PacBio using Seq2scFv (https://github.com/ngs-ai-org/seq2scfv). </p> <p>Raw files were obtained from publicly available dataset generated by Nannini and colleagues in "Combining phage display with SMRTbell next-generation sequencing for the rapid discovery of functional scFv fragments." <em>MAbs</em>. Vol. 13. No. 1. Taylor & Francis, 2021.</p> <p>The results of the annotation are organized in directories. These correspond to the different steps of the tutorial presented in the Seq2scFv repository. </p> <p>├── 1.Preprocessed<br>├── 2.Catalogued<br>├── 3.vscan<br>├── 4.scFv_split<br>├── 5.Linkers<br>├── 6.Flags<br>├── 7.Counts<br>└── focus_libs.txt</p> <p>This entry also contains the code provided in the GitHub repository.</p>
Utilizing Long-read Sequencing to Investigate the EGFR Landscape of EGFR Positive Lung Cancer Patients
ClinicalTrials.gov study NCT06659458. IPD Sharing: YES. Countries: 1. Publications: 0.
Data from: De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii
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Profiling epigenetic aging at cell-type resolution through long-read sequencing
GEO Series GSE296282. Homo sapiens. 5 samples. Type: Methylation profiling by high throughput sequencing.
Nanopore long-reads sequencing of hepatitis A virus RNAs
GEO Series GSE293395. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Direct long-read RNA sequencing of Raji cells
GEO Series GSE243920. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
Non-destructive enzymatic deamination enables single molecule long read sequencing for the determination of 5-methylcytosine and 5- hydroxymethylcytosine at single base resolution
GEO Series GSE141908. Mus musculus. 16 samples. Type: Other; Methylation profiling by high throughput sequencing.
High-resolution transcriptome analysis with long-read RNA sequencing
GEO Series GSE57862. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.