Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
63
datasets available to search
ShareScore release 0.9.0
Dataset results
63 results for “ncbi”
3682 E. coli assemblies from NCBI
<p>This is a dataset of 3682 E. coli assemblies downloaded from NCBI circa 2020 aiming to replicate the E. coli dataset in the paper "Succinct colored de Bruijn graphs" by Muggli et al. <a href="https://doi.org/10.1093/bioinformatics/btx067">https://doi.org/10.1093/bioinformatics/btx067</a>. The data is in 3682 FASTA files, one for each assembly. The uncompressed size is 18GB.</p>
Species abundance information improves sequence taxonomy classification accuracy - HMP and NCBI data
<p>Data used to test <a href="https://library.qiime2.org/plugins/q2-clawback/">q2-clawback</a> using taxonomic weights derived from shotgun sequencing experiments.</p> <p>Includes reference sequences and taxonomies derived from the NCBI RefSeq database[1] and paired amplicon and shotgun sequencing results downloaded from the Human Microbiome Project[2].</p> <p>References<br> 1. O’Leary, N. A. et al. en. Nucleic Acids Res. 44, D733–45 (2016).<br> 2. Huttenhower, C. et al. Nature 486, 207 (2012).</p>
NCBI Taxonomy for DH (TRAM-796): NCBI Taxonomy for DH (TRAM-796)
Bacteria and microbial eukaryote branches from the NCBI taxonomy.<p></p>NCBI with most surrogates, viruses, viroids, embryophytes, fungi, and animals removed. Data sets for the assembly of the EOL dynamic hierarchy.
NCBI Taxonomy Harvest (TRAM-795): NCBI_Taxonomy_Harvest_no_vernaculars.tar.gz
NCBI hierarchy with many surrogates removed.<p></p>vernaculars removed and root node made parentless Data sets for the assembly of the EOL dynamic hierarchy.
NCBI Taxonomy Harvest (TRAM-795): NCBI_Taxonomy_Harvest.tar.gz
NCBI hierarchy with many surrogates removed.<p></p>Data sets for the assembly of the EOL dynamic hierarchy.
NCBI
As a U.S. national resource for molecular biology information, NCBI__s mission is to develop new information technologies to aid in the understanding of fundamental molecular and genetic processes that control health and disease. The NCBI taxonomy database contains the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence.
Assembled "juvenile head region" transcriptome from the hagfish Eptatretus burgeri (NCBI GenBank Accession: SRX2541845)
<p>1) The raw reads were dwonloaded from NCBI GenBank (SRA run accession: (SRR5234495) with sratoolkit.</p> <p>2) The assembly was performed with Trinity with the folllowing parameters:</p> <p>Trinity --seqType fq --max_memory 100G --left eb-hf-head-region-SRR5234495/eb-hf-head-region-SRR5234495_1.fastq --right eb-hf-head-region-SRR5234495/eb-hf-head-region-SRR5234495_1.fastq --CPU 10 --output trinity-transcriptome-eb/</p> <p>3) ORFs were predeicted with TransDecoder with the following settings:</p> <p>TransDecoder.LongOrfs -t transcriptome-eb-hf-head-region.fasta</p> <p>TransDecoder.Predict -t transcriptome-eb-hf-head-region.fasta</p> <p> </p>
FIGURE 2 in The disconnect between DNA and species names: lessons from reptile species in the NCBI taxonomy database
FIGURE 2. Growth of reptile species numbers in the Reptile Database and NCBI Taxonomy/ GenBank. "Genbank binomial species" are those that have a valid equivalent in the Reptile Database while GenBank all reptile "species" include all other unique names, even when their identity is not clear (or not reported to GenBank, see Table 1).
FIGURE 1 in The disconnect between DNA and species names: lessons from reptile species in the NCBI taxonomy database
FIGURE 1. Relationship between databases, such as the NCBI Taxonomy, the Reptile Database, and other taxonomic databases and data sources. Some of the resources shown are examples for other data resources not shown. Arrows indicate data flow or referencing (linking) between databases. For instance, iNaturalist uses names from the Reptile Database, with the latter linking back directly to iNaturalist species pages. Arrows to and from collections (and collection data aggregators such as VertNet) indicate cross-referencing of specimens, but not necessarily hyperlinks.
Cenote-Taker2 NCBI_CD hhsuite Database
<p>NCBI's CD database formatted for hhsuite searches</p>
NCBI Nt (Nucleotide) database FASTA file from 2017-10-26
<p>This FASTA file is the NCBI Nt (Nucleotide) database (public domain) used for holistic metagenomic screening of ancient DNA data at the Department of Archaeogenetics at the Max Planck Institute for the Science of Human History. We offer here the FASTA file used to construct MALT databases (https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/malt/), which are generally too large for uploading. Please see each relevent publications that use the database for MALT database construction commands.</p> <p>NCBI does not retain older versions of this database which is why this has been uploaded here. It was downloaded on 2017-10-26 12:39 from: ftp://ftp-trace.ncbi.nih.gov/blast/db/FASTA/nt.gz. The NCBI Nt database is released into the public domain as per https://www.ncbi.nlm.nih.gov/home/about/policies/.</p> <p> </p>
NCBI bacterial query sequences
<p>Bacterial sequences downloaded from the NCBI assembly database. The file qseqs78M.fna includes Escherichia coli, Klebsiella, and Streptococcus sequences that were aligned to E.coli pan-genome. The file qseqs29M.fna includes randomly selected sequences from the GenBank assemblies that were aligned to GenBank pan-genome including all bacterial species.</p>
Melon database (NCBI taxonomy)
<div> <div>RefSeq R229 with 63,660 species and 423,988 genomes.</div> <div> <div> </div> </div> </div> <div> <div> </div> </div>
Galaxy Training Network - Screening assembled genomes for contamination using NCBI FCS
<p>This is a toy dataset generated from an assembled yeast genome (Saccharomyces cerevisiae; GCA_000146045.2) with contaminants added from human, Pseudomonas aeruginosa, and Illumina PCR primers.</p>
All Virus sequences originated for VIROPLANT by all partners and deposited in NCBI
<p>All Virus sequences originated for VIROPLANT by all partners and deposited in NCBI</p>
NCBI database for Lysobacteraceae network of gene sharing study
<p>NCBI database for Lysobacteraceae network of gene sharing study</p>
Metagenomic and metatranscriptomics data for Bathymodiolus mussel and deep-sea sponge associated symbionts deposited in NCBI, IMG and other databases
<p>Metagenomic data for the sulfur- and methane-oxidizing symbionts of <em>Bathymodiolus</em> mussels and different sponge species deposited in the Integrated Microbial Genomes (IMG) database of the DOE Joint Genome Institute (http://img.jgi.doe.gov/) and NCBI until October 2017.</p>
Supplementary material 1 from: Macher J, Macher T, Leese F (2017) Combining NCBI and BOLD databases for OTU assignment in metabarcoding and metagenomic datasets: The BOLD_NCBI _Merger. Metabarcoding and Metagenomics 1: e22262. https://doi.org/10.3897/mbmg.1.22262
The supplementary material contains the BOLD_NCBI_Merger script, the needed folder structure and the tutorial explaining how to use the script
NCBI taxonomy dump used for specI and mOTUs
<p>NCBI taxonomy dump used for:</p> <p>- mOTUs 2.5.0</p> <p>- progenomes 2</p>
Comprehensive Structural Variant Benchmark Dataset: 1100 VCF files from long-read sequencing of 10 NCBI individuals
<p>We initially collected 10 NCBI individuals: HG002 family pedigree data (HG002 [son], HG003 [father], HG004 [mother]), the HG005 family pedigree data (HG005 [son], HG006 [father], HG007 [mother]), the NA12878 subject, the HG00096 subject, the HG00512 subject and the CHM13 subject. Then we used PacBio (CLR: Continuous Long Read, CCS: Circular Consensus Sequencing) and Nanopore (ONT) platforms, 5 aligners and 10 callers to construct the pipelines, with most parameters set to default values. After that, except for 6 invalid pipelines(pbmm2-Nanovar, lra-Picky, lra-delly, lra-NanoVar, lra-NanoSV, lra-pbsv), we obtain 1100 VCF files.</p>
ScienceDex guides
Understand access before you commit
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.