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71 results for “Metagenome assembled genome”
Metagenome-assembled genomes(MAGs) generated from CRC human gut (PRJEB27928).
<p>MAGs generated from CRC human gut (PRJEB27928) with Maxbin2, VAMB, Metabat2, SemiBin(single-sample binning) and VAMB, SemiBin(multi-sample binning).</p> <p>Single-sample binning: Maxbin2.tar.gz, Metabat2.tar.gz, VAMB.tar.gz and SemiBin(_pretrain).tar.gz. </p> <p>Multi-sample binning: VAMB_multi.tar.gz and SemiBin_multi.tar.gz.</p>
Metagenome-assembled genomes(MAGs) generated from dog gut (PRJEB20308).
<p>MAGs generated from dog gut (PRJEB20308) with Maxbin2, VAMB, Metabat2, SemiBin(single-sample binning) and VAMB, SemiBin(multi-sample binning).</p> <p>Single-sample binning: Maxbin2.tar.gz, Metabat2.tar.gz, VAMB.tar.gz and SemiBin(_pretrain).tar.gz. </p> <p>Multi-sample binning: VAMB_multi.tar.gz and SemiBin_multi.tar.gz.</p>
Metagenome-assembled genomes(MAGs) generated from ocean (PRJEB1787).
<p>MAGs generated from ocean (PRJEB1787) with Maxbin2, VAMB, Metabat2, SemiBin(single-sample binning) and VAMB, SemiBin(multi-sample binning).</p> <p>Single-sample binning: Maxbin2.tar.gz, Metabat2.tar.gz, VAMB.tar.gz and SemiBin(_pretrain).tar.gz. </p> <p>Multi-sample binning: VAMB_multi.tar.gz and SemiBin_multi.tar.gz.</p>
Oceanic Prokaryotes Metagenome-Assembled Genomes reconstructed using metagenomic distances
<p>Sets of reconstructed Metagenome-Assembled Genomes (MAGs) from Tara Oceans dataset. The reconstructed MAGs belong to Magneto paper: https://doi.org/10.1128/msystems.00432-22</p> <p>The dataset is composed of 93 oceanic metagenomes sampled from non-polar oceanic regions.</p> <p>The Metagenomic Distance MAGs were reconstructed following a co-assembly protocol driven by nucleotidic composition similarity, as detailed in the publication.</p> <p>The Oceanic Region MAGs were reconstructed by co-assembly of samples belonging to the same Oceanic Regions.</p> <p>The file clusters.tsv sum up the metagenomic distance cluster and the oceanic region each sample belongs to.</p>
179 high quality metagenome-assembled genomes sequences and annotations
<p>We analyzed seven sediment samples collected adjacent to ferromanganese nodules from the Clarion–Clipperton Fracture Zone (CCFZ) in the eastern Pacific Ocean. Through deep metagenomic sequencing, assembly, and binning, we reconstructed 179 high quality metagenome-assembled genomes (MAGs). This archive contains these genomes sequences and annotations. </p>
Metagenomes and metagenome-assembled genomes from Onthophagus taurus
Open the record for dataset details and reuse information.
Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features"
<p>Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features" (submitted to Nature Communications)</p>
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>
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>
Expanded catalog of metagenome-assembled genomes reveals resistome characteristics athletic performance- associated microbes in horse
<p><strong>Background</strong><br> As a domesticated species vital to humans, horses are raised worldwide as a source of mechanical energy for sports, leisure, food production, and transportation. The gut microbiota plays an important role in the health, diseases, athletic performance, and behaviour of horses.<br> <strong>Results</strong><br> Here, using approximately 2.2 Tb of metagenomic sequencing data from gut samples from 242 horses, including 110 samples from the caecum and 132 samples from the rectum (faeces), we assembled 4142 microbial metagenome-assembled genomes (MAG), 4015 (96.93%) of which appear to correspond to new species. From long-read data, we successfully assembled 13 circular whole-chromosome bacterial genomes representing novel species. The MAG contained over 313,568 predicted carbohydrate-active enzymes (CAZy), over 59.77% of which had low similarity match in CAZy public databases. High abundance and diversity of antibiotic resistance genes (ARG) were identified in the MAG, likely showing wide use of antibiotic in the management of horse. The abundances of at least 36 MAG (e.g. MAG belonging to Lachnospiraceae, Oscillospiraceae, and Ruminococcus) were higher in elite racehorses than that in normal horses. These MAG enriched in racehorses contained every gene in a major pathway for producing acetate and butyrate by fiber fermentation, presenting potential for greater amount of short-chain fatty acids available to fuel athletic performance.<br> <strong>Conclusions</strong><br> Overall, we assembled 4142 MAG from short- and long-read sequence data in the horse gut. Our dataset represents an exhaustive microbial genome catalog for the horse gut microbiome and provides a valuable resource for discovery of performance-enhancing microbes and studies of horse gut microbiome.</p>
Prokaryotic gene catalog, prokaryotic Metagenome-Assembled Genomes (MAGs) and taxonomic profiling of metagenomic data of NEREA Augmented Observatory
<p>The NEREA_metaG directory is dedicated to the in-depth analysis of NEREA microbial communities using metagenomic sequencing data. </p> <p><strong>Gene catalog:</strong> This directory contains the gene catalog compiled from metagenomic data, which includes: Protein and nucleotide sequence files for genes; Cluster files grouping similar genes; Annotation files mapping genes to KEGG pathways; Normalized gene abundance profiles.</p> <div><strong>MAGs:</strong> Directory for Metagenome-Assembled Genomes (MAGs). It contains comprehensive annotation files for the MAGs, providing insights into gene functions, metabolic pathways, and other genomic features. It also contains the individual MAGs categorized by sample origin. Each MAG is stored in a compressed FASTA format.</div> <p><strong>mOTUs</strong>: Contains files related to microbial taxonomic units identified and quantified using the mOTUs profiler. </p>
Phoronid-associated metagenome assembled genomes
<p>Metagenome assembled genomes (MAGs) associated with:</p> <p>Phoronids and their tubes harbor distinct microbiomes compared to surrounding sediment</p> <p>Analysis, code, intermediate and supporting files are archived here: <a href="../doi/10.5281/zenodo.11225270">10.5281/zenodo.11225270</a><br><br>This archive contains:<br>(i) Five fasta files representing the MAGs described in the above titled work<br>(ii) Metadata file describing the five MAGs (i.e., Table 1 from the above work)</p>
Metagenome assembled genomes for Gilbert et al. 2024 ARW Pond study
<p>MAG assemblies used for GIlbert 2024 ARW Pond Microbiome study. Each MAG assembly has a separate ".fa" file. </p>
Dataset for "Metagenome-Assembled Bacterial Genomes from Long Accurate Reads Associated with Capilliphycus salinus ALCB114379"
<p>We present the raw genomic dataset of the marine cyanobacterium Capilliphycus salinus ALCB114379, sequenced using PacBio HiFi long-read technology.</p> <p><strong>ABSTRACT</strong></p> <p><span>We report the complete genome sequences of five bacteria linked to the marine cyanobacterium <em>Capilliphycus salinus</em> ALCB114379 from the phylum Pseudomonadota. This genetic diversity offers new insights into the genetic landscape and potential symbiotic relationships of cyanobacteria-associated microbiota.</span></p>
Interactive heatmaps for metagenome assembled genome (MAG) metagenomic potential and metaproteomic peptide recruitment
<p>Interactive heatmaps for supplementary figure 1 and supplementary figure 4 from publication to be submitted titled "<strong>Microbial genome-resolved metaproteomic analyses frame intertwined carbon and nitrogen cycles in river hyporheic sediments". </strong></p>
Twenty-five metagenome assembled genomes recovered from the gut microbiome of the domestic ferret, Mustela putorius
<p>This is metadata provided in a single excel file for 25 unique metagenome assembled genomes (MAGs) recovered from the gut microbiome of three domestic ferrets (<em>Mustela putorius</em>). Details on both MAG and host ferret metadata, as well as information on sample collection, DNA sequencing, and bioinformatic processing can be found here, in association with the American Society for Microbiology Resource Announcement by Amundson et al. (in prep). </p>
Metagenome Assembly Genome Bins.tar
<p>Metagenome assembly genome bins of cattle</p>
Figure 3 in Whole and nearly complete mitochondrial genomes of an endemic and endangered neotropical rabbit (Romerolagus diazi) assembled using non-invasive eDNA metagenomics (field droppings)
Figure 3. Phylogenetic analysis of Romerolagus diazi and related species in the family Leporidae. Totalevidence phylogenetic tree obtained from ML analysis based on a concatenated alignment of amino acids of the 13 protein-coding genes present in the mitochondrial genome of representatives of the family Leporidae. In the analysis, two species of the family Ochotonidae were used as the outgroup. Numbers above or below the branches represent bootstrap values. Photo credit: J.A. Guerrero.
Figure 2 in Whole and nearly complete mitochondrial genomes of an endemic and endangered neotropical rabbit (Romerolagus diazi) assembled using non-invasive eDNA metagenomics (field droppings)
Figure 2. Relative codon usage analysis for protein coding genes (PCGs) in the mitochondrial genome of Romerolagus diazi assembled from eDNA (field collected droppings, sample SRR14209493 [top] and SRR14209494 [bottom]).
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.