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181 results for “Nanopore sequencing”
Data from: A first look at the Oxford Nanopore MinION sequencer
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Data from: Estimating bloodstain age in the short term based on DNA fragment length using nanopore sequencer
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Data from: Chromosome-level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of Nanopore Sequencing, Bionano and Hi-C technology
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Data from: De novo sequencing and variant calling with nanopores using PoreSeq
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.
Data from: De novo assembly of a chromosome-level reference genome of red spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C
The red spotted grouper Epinephelus akaara (E. akaara) is one of the most economically important marine fish in China, Japan and Southeast Asia, and is a threatened species. The species is also considered a good model for studies of sex-inversion, development, genetic diversity and immunity. Despite its importance, molecular resources for E. akaara remain limited and no reference genome has been published to date. In this study, we constructed a chromosome-level reference genome of E. akaara by taking advantage of long-read single molecule sequencing and de novo assembly by Oxford Nanopore Technologies (ONT) and Hi-C. A red-spotted grouper genome of 1.135 Gb was assembled from a total of 106.29 Gb polished Nanopore sequence (GridION, ONT), equivalent to 96-fold genome coverage. The assembled genome represents 96.8% completeness (BUSCO) with a contig N50 length of 5.25 Mb and a longest contig of 25.75 Mb. The contigs were clustered and ordered onto 24 pseudo-chromosomes covering approximately 95.55% of the genome assembly with Hi-C data, with a scaffold N50 length of 46.03 Mb. The genome contained 43.02% repeat sequences and 5,480 non-coding RNAs. Furthermore, after mining several RNA-seq datasets, 23,809 (99.5%) genes were functionally annotated from a total of 23,924 predicted protein-coding sequences. The high-quality chromosome-level reference genome of E. akaara was assembled for the first time and will be a valuable resource for molecular breeding and functional genomics studies of red-spotted grouper in the future.
Rapid multiplexed nanopore amplicon sequencing to distinguish Plasmodium falciparum recrudescence from new infection in antimalarial drug trials
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Nanomotif: Identification and Exploitation of DNA Methylation Motifs in Metagenomes using Oxford Nanopore Sequencing
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Datasets used in "Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat"
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Supplementary Material. Single laboratory evaluation of the Q20+ nanopore sequencing kit for bacterial outbreak investigations
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TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing
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Supporting data for Comparison of Oxford Nanopore and Illumina sequencing for SARS-CoV-2 variant monitoring in wastewater
<p>This dataset contains the FASTQ files used in the paper <em>Comparison of Oxford Nanopore and Illumina sequencing for SARS-CoV-2 variant monitoring in wastewater</em>. </p> <p>The FASTQ files are classified in 2 different folders: MinION and MiSeq. Inside the MinION folder, there are two more folders, one for the R9.4.1 flow cell data and the other for the R10.4.1 flow cell data. </p> <p>Twist synthetic RNA mixtures are named as mix1, mix2, etc. </p> <p>Twist synthetic RNA corresponding to the Wuhan sequence is named as mix11_WH</p> <p>Wastewater samples are named as WWTP_1, WWTP_2, etc. </p>
Nanopore signals corresponding to all negative sample sequences
<p>This dataset contains the nanopore signals of the negative samples in all datasets.</p>
Data from: De novo assembly of a chromosome-level reference genome of red spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C
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Data from: De novo sequencing and variant calling with nanopores using PoreSeq
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Nanopore long-reads sequencing of hepatitis A virus RNAs
GEO Series GSE293395. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Post-transcriptional regulation by the gut microbiota decoded by nanopore direct RNA sequencing [RNA methylation]
GEO Series GSE261724. Mus musculus; Homo sapiens. 14 samples. Type: Other.
Nanopore RNA sequencing in S. cerevisiae strains defective for decapping and deadenylation
GEO Series GSE211782. Saccharomyces cerevisiae. 6 samples. Type: Expression profiling by high throughput sequencing.
Nanopore Sequencing for the screening of Myeloid and Lymphoid neoplasms with eosinophilia and rearrangement of PDGFRa, PDGFRb, FGFR1 or PCM1-JAK2.
GEO Series GSE185446. Homo sapiens. 12 samples. Type: Other.
PoreMeth2: decoding the evolution of methylome alterations with Nanopore sequencing. [WGS]
GEO Series GSE277455. Homo sapiens. 6 samples. Type: Other.
Analysis of HIV-1 transcriptome in different cell models with nanopore sequencing
GEO Series GSE138425. Homo sapiens. 20 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)
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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.