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.
915
datasets available to search
ShareScore release 0.7.1
Dataset results
915 results for “metagenomics”
Supplementary material 3 from: Ahmed M, Slos D, Holovachov O (2024) Assessing the diversity of nematodes in the Store Mosse National Park (Sweden) using metabarcoding. Metabarcoding and Metagenomics 8: e111307. https://doi.org/10.3897/mbmg.8.111307
Proportions of total ASVs assigned to various nematode families including those unassigned at the family level across all samples
Integrating Metagenomic and Metabolomic Insights into Host-Microbe Connections for Gut-Lung Axis in Childhood Asthma
Open the record for dataset details and reuse information.
Gene catalogs and KEGG annotation related to root metagenomic samples
<p><span>Reference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of </span><span>crop </span><span>root microbiome</span><span>s</span><span>. Combining high-throughput bacterial cultivation with metagenomic sequencing, we constructed comprehensive bacterial and viral genome collections from the roots of wheat, rice, maize, and Medicago. The crop root bacterial genome collection (CRBC) significantly expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes, with 6,699 bacterial genomes (</span><span>68.9 % </span><span>from isolates) </span><span>and 1,817 novel species,</span><span> expanding crop root bacterial diversity by </span><span>290.6%</span><span>. The crop root viral genome collection (CRVC) contains 9,736 nonredundant viral genomes, with 1,572 previously unreported genus-level clusters in crop roots. From these data, we identified conserved bacterial </span><span>functions</span><span> enriched in root microbiomes across soils and host species and uncovered previously unexplored bacteria–virus </span><span>connections</span><span> in crop root ecosystems. Together, the CRBC and CRVC serve as valuable resources for investigating microbial mechanisms and applications, supporting sustainable agriculture. </span></p> <p> </p> <p>The gene sets of 14 datasets are available under this accession.</p>
Microbial Genomes and Metagenomes Workshop
Open the record for dataset details and reuse information.
Metagenome-assembled genomes generated from dog dental plaque microbiome
<p>Metagenome-assembled genomes generated from dog dental plaque microbiome from the study "Newly identified species from the dog dental plaque microbiome highlight little overlap with humans"</p>
Metagenome-Assembled Genomes of 2_1_SS_W3_F1
<p>This dataset is featured in the data report <em>"Exploring the Taxonomical and Functional Profiles of Marine Microorganisms in Submarine Groundwater Discharge Vent Water from Mabini, Batangas, Philippines through Metagenome-Assembled Genomes."</em> The assembled genomes were taxonomically identified and analyzed for nutrient metabolism genes involved in biogeochemical cycles, as well as potential biosynthetic gene clusters of medical relevance. The dataset includes generated bins with corresponding RAST annotations.</p>
Bins with greater than 50% completeness and less than 10% contamination from the paper "Benchmarking Metagenomic Binning Tools on Real Datasets Across Sequencing Platforms and Binning Modes".
<p>These bins, which exhibit greater than 50% completeness and less than 10% contamination, including MQ, NC, and HQ bins, were recovered from seven different data-binning combinations across five real-world datasets.</p> <p>CheckM2 results for the bins generated from each sample were also provided to corroborate the findings.</p> <p>Completeness and contamination were evaluated using CheckM 2 (version 1.0.2). We noted that the results from running CheckM2 may exhibit slight variations, but these differences do not affect the overall assessment.</p>
DRAMMA: A multifaceted machine learning approach for novel antimicrobial resistance gene detection in metagenomic data (dataset 2 of 2)
<p>Dataset for the support of a journal publication. </p> <p>Part 2/2 of a dataset used for running and training the ML model.</p> <p>Part 1 is available at <a href="https://doi.org/10.5281/zenodo.14513933">10.5281/zenodo.14513933</a></p> <p>The code associated with this publication is available at: https://github.com/burstein-lab/DRAMMA </p>
DRAMMA: A multifaceted machine learning approach for novel antimicrobial resistance gene detection in metagenomic data (dataset 1 of 2)
<p>Dataset for the support of a journal publication. </p> <p>Part 1/2 of a dataset used for running and training the ML model.</p> <div> <div>Part 2 is available at <a href="https://doi.org/10.5281/zenodo.14524613">10.5281/zenodo.14524613</a></div> <div> </div> </div> <p>The code associated with this publication is available at: https://github.com/burstein-lab/DRAMMA </p>
Cave Metagenome Protein Catalogue
<p>The concatenated output of protein-level assembly (using PLASS) of available cave metagenomes.</p>
Metagenome-assembled genomes for "Impacts of beaver ponds on biogeochemical cycling of organic nitrogen within a fire-impacted watershed"
<p>This dataset includes all of the metagenome-assembled genomes (MAGs) used in Roth et al.: "Impacts of beaver ponds on biogeochemical cycling of organic nitrogen within a fire-impacted watershed" (in prep.). The metagenomic sequencing was completed on a suite of sediment samples collected from the sediment-water interface of beaver ponds within wildfire burn scars.</p>
Full Dataset S4 - Metagenomes associated with the methane ice worm (Sirsoe methanicola)
<p><strong>FULL DATASET S4</strong>. IDs and alignment statistics of each read from A) worm fragments sequenced by HiSeq (Library W), B) gut contents sequenced by HiSeq (Library G), and C) gut contents sequenced by MiSeq (Library G-Mi) matching 16S rRNA gene sequences sequenced from methanogenic habitats (<strong>Dataset S3</strong>) using NCBI Magic-BLAST. The results were deduplicated to only show paired-reads. For multi-mapping reads, the alignment with the highest score is shown. The alignment statistics were further summarized in D) Library W, E) Library G, and F) Library G-Mi to show the total number of reads, mean % identity, min % identity, and max % identity mapped to each reference sequence. G) Predicted taxonomy for reference 16S rRNA gene sequences in <strong>Dataset 3 </strong>produced by QIIME2's VSEARCH-based consensus taxonomy classifier and sci-kit learn classifier.</p>
Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: viruses, plasmids, and more
<p>Supplementary Table 2-1. Samples and assembly summary <br> Supplementary Table 2-2. CRISPR-targeted TR sequence summary</p>
Supplementary material 1 from: Chua PYS, Carøe C, Crampton-Platt A, Reyes-Avila CS, Jones G, Streicker DG, Bohmann K (2022) A two-step metagenomics approach for the identification and mitochondrial DNA contig assembly of vertebrate prey from the blood meals of common vampire bats (Desmodus rotundus). Metabarcoding and Metagenomics 6: e78756. https://doi.org/10.3897/mbmg.6.78756
A two-step metagenomics approach for prey identification from the blood meals of common vampire bats (Desmodus rotundus)
Viral metagenomics reveals persistent as well as dietary acquired viruses in Antarctic fur seals
<p>Antarctic fur seal virome</p>
Downsampled metagenomic datasets for the metaFlye tutorial
<p>Downsampled metagenomic datasets for the metaFlye tutorial</p>
Supplementary material 3 from: Jeunen G-J, Lipinskaya T, Gajduchenko H, Golovenchik V, Moroz M, Rizevsky V, Semenchenko V, Gemmell NJ (2022) Environmental DNA (eDNA) metabarcoding surveys show evidence of non-indigenous freshwater species invasion to new parts of Eastern Europe. Metabarcoding and Metagenomics 6: e68575. https://doi.org/10.3897/mbmg.6.e68575
Reference databases generated by ecoPCR and used by ecotag for taxonomy assignment of OTUs for fish and crustacean eDNA results
Metagenome species-level index for Themisto v2.1.0
<p>Index for Themisto >v2.0.0 or newer containing many species.</p> <p>Changelog:<br> v1.0.1: compressed the index more, reducing total size from 8GB to 3.3GB</p>
Data from: Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics
High-throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set of 214 mitochondrial sequences longer than 3000 bp was generated and used to estimate a well-supported phylogenetic tree of the order Coleoptera. Shorter sequences, including cox1 barcodes, were placed on this mitogenomic tree. Raw Illumina reads were mapped against all available sequences to test for species present in local samples. This approach simultaneously established the species richness, phylogenetic composition and community turnover at species and phylogenetic levels. We find a strong signature of vertical structuring in soil fauna that shows high local community differentiation between deep soil and superficial horizons at phylogenetic levels. Within the two vertical layers, turnover among regions was primarily at the tip (species) level and was stronger in the deep soil than leaf litter communities, pointing to layer-mediated drivers determining species diversification, spatial structure and evolutionary assembly of soil communities. This integrated phylogenetic framework opens the application of phylogenetic community ecology to the mesofauna of the soil, among the most diverse and least well-understood ecosystems, and will propel both theoretical and applied soil science.
Supplementary material 3 from: Swenson SJ, Eichler L, Hörren T, Kolter A, Köthe S, Lehmann GUC, Meinel G, Mühlethaler R, Sorg M, Gemeinholzer B (2022) The potential of metabarcoding plant components of Malaise trap samples to enhance knowledge of plant-insect interactions. Metabarcoding and Metagenomics 6: e85213. https://doi.org/10.3897/mbmg.6.85213
Supplementary material 3 from: Swenson SJ, Eichler L, Hörren T, Kolter A, Köthe S, Lehmann GUC, Meinel G, Mühlethaler R, Sorg M, Gemeinholzer B (2022) The potential of metabarcoding plant components of Malaise trap samples to enhance knowledge of plant-insect interactions. Metabarcoding and Metagenomics 6: e85213. https://doi.org/10.3897/mbmg.6.85213
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.