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Dataset results
915 results for “metagenomics”
Metagenomic bins and biosynthetic gene clusters in gut bacteria of turtle ants
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Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs
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Resurrection of a global, metagenomically defined gokushovirus
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Dataset S2: Global Synechococcus pigment type distribution from metagenomes with co-located mixed layer depths and sea surface properties
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Supplementary material 6 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925
Figure S6. Average nucleotide diversity for all four datasets of shared OTUs seperated according to sample sites and EPT (Ephemeroptera, Plecoptera, Trichoptera) and PR ('Pollution Resistant') taxa
Supplementary material 5 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925
Figure S5. Average haplotype diversity for all four datasets of shared OTUs seperated according to sample sites and EPT (Ephemeroptera, Plecoptera, Trichoptera) and PR ('Pollution Resistant') taxa
Supplementary material 7 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925
Figure S7 – part 1. Haplotype network of the two most frequent EPT (Ephemeroptera, Plecoptera, Trichoptera) and PR ('Pollution Resistant') taxa
Supplementary material 4 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925
Figure S4. Average haplotype number per OTU for the four different datasets of shared OTUs. Datasets are split into EPT (Ephemeroptera, Plecoptera, Trichoptera) and PR ('Pollution Resistant') taxa
Supplementary material 3 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925
Figure S3. Average haplotype number per OTU for the four different datasets of shared OTUs. Values are illustrated for all sample sites including all shared OTUs
Supplementary material 2 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925
Figure S2. Four different datasets including shared OTUs between the different river systems (Emscher-Ennepe-Sieg, Emscher-Ennepe, Emscher-Sieg, Sieg-Ennepe). Number of OTUs is illustrated with taxonomic assignment on order level
Supplementary material 1 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925
Figure S1. Total number of aquatic macroinvertebrate individuals per sample and season plotted against the average haplotype number per OTU. Different colours indicate the three river systems
In situ microcosms deployed at the coast of British Columbia (Canada) to study dilbit weathering and associated microbial communities under marine conditions. (Metagenomic data support).
<p>This file repository contains the co-assembly of all samples from the manuscript entitled "In situ microcosms deployed at the coast of British Columbia (Canada) to study dilbit weathering and associated microbial communities under marine conditions". It also contains predicted genes sequence files in faa (fasta amino acids) and fna (fasta nucleic acids) formats.</p>
Supplementary material 2 from: Nugent CM, Adamowicz SJ (2020) Alignment-free classification of COI DNA barcode data with the Python package Alfie. Metabarcoding and Metagenomics 4: e55815. https://doi.org/10.3897/mbmg.4.55815
File S2 – Python script for custom grid search of hyperparameters for optimization of the neural network
Supplementary material 3 from: Nugent CM, Adamowicz SJ (2020) Alignment-free classification of COI DNA barcode data with the Python package Alfie. Metabarcoding and Metagenomics 4: e55815. https://doi.org/10.3897/mbmg.4.55815
File S3 – The parameters utilized in the grid search for each of the five machine learning algorithms tested in the design of the Alfie package
Supplementary material 4 from: Nugent CM, Adamowicz SJ (2020) Alignment-free classification of COI DNA barcode data with the Python package Alfie. Metabarcoding and Metagenomics 4: e55815. https://doi.org/10.3897/mbmg.4.55815
File S4 – Jupyter notebook with tutorial demonstrating how to apply the Alfie classifier in the Python programming language, and how to train custom alignment-free classifiers using the Alfie training module
Supplementary material 2 from: Macher J-N, Drakou K, Papatheodoulou A, Hoorn B, Vasquez M (2020) The mitochondrial genomes of 11 aquatic macroinvertebrate species from Cyprus. Metabarcoding and Metagenomics 4: e58259. https://doi.org/10.3897/mbmg.4.58259
Supplementary tables showing reads numbers, coverage and length of mitochondrial genomes, and length and blast results of 18S and 28S rRNAs
Unveiling viruses associated to gastroenteritis using metagenomics approach
<p>Metagenomic analysis of viruses in feces.</p>
Urban wastewater virome by viral metagenomics and target enrichment sequencing
<p>Metagenomic analysis of virus in raw sewage.</p>
Supplementary material 1 from: Basset Y, Donoso DA, Hajibabaei M, Wright MTG, Perez KHJ, Lamarre GPA, De León LF, Palacios-Vargas JG, Castaño-Meneses G, Rivera M, Perez F, Bobadilla R, Lopez Y, Ramirez JA, Barrios H (2020) Methodological considerations for monitoring soil/litter arthropods in tropical rainforests using DNA metabarcoding, with a special emphasis on ants, springtails and termites. Metabarcoding and Metagenomics 4: e58572. https://doi.org/10.3897/mbmg.4.58572
Methodological considerations for monitoring soil/litter arthropods in tropical rainforests using DNA metabarcoding, with a special emphasis on ants, springtails and termites
Supplementary material 1 from: Weigand AM, Desquiotz N, Weigand H, Szucsich N (2021) Application of propylene glycol in DNA-based studies of invertebrates. Metabarcoding and Metagenomics 5: e57278. https://doi.org/10.3897/mbmg.5.57278
Overview of DNA-based studies of invertebrates applying propylene glycol, sorted by year and taxonomic group
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.