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103 results for “metagenomes assembly”
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]).
Figure 1 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 1. Circular DNA mitochondrial genome map of Romerolagus diazi assembled from eDNA (field collected droppings, sample SRR14209493). The annotated map depicts 13 protein-coding genes (PCGs), two ribosomal RNA genes (rrnS: 12S ribosomal RNA and rrnL: 16S ribosomal RNA), 22 transfer RNA (tRNA) genes, and the putative control region (not annotated). Photo credit: J.A. Guerrero.
Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia
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Co-assembly of 98TBs of metagenomes from human gut using exascale assembler MetaHipMer
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Time-series drinking water metagenomes: Assemblies & MAGs
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Supporting data for the manuscript "metaFlye: scalable long-read metagenome assembly using repeat graphs"
<p>Genome assemblies, simulated datasets and evaluations described in the manuscript "metaFlye: scalable long-read metagenome assembly using repeat graphs".</p>
Supplementary data (simulated metagenome set 1) to accompany "phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes"
<p>Comparison of SSU rRNA read extraction and targeted assembly from simulated shotgun metagenome of divergent bacterial species.</p> <p>The phyloFlash software is available from https://github.com/HRGV/phyloFlash. Examples were generated with phyloFlash v3.3b.</p>
Supplementary data (comparison of multiple metagenomes) to accompany "phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes"
<p>Usage example for phyloFlash, comparison of multiple metagenomes by SSU rRNA taxonomic profile. </p> <p>The phyloFlash software is available from https://github.com/HRGV/phyloFlash. Examples were generated with phyloFlash v3.3b.</p>
Supplementary data (low-diversity metagenome and reference database completeness) to accompany "phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes"
<p>Comparison of phyloFlash and Matam on low-diversity platyhelminth metagenome, showing effect of reference database completeness on results. </p> <p>The phyloFlash software is available from https://github.com/HRGV/phyloFlash. Examples were generated with phyloFlash v3.3b.</p>
Supplementary data (Tara Oceans metagenomes) to accompany "phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes"
<p>Comparison of SSU rRNA read extraction and targeted assembly by phyloFlash and Matam from environmental metagenomes from the Tara Oceans dataset.</p> <p>The phyloFlash software is available from https://github.com/HRGV/phyloFlash. Examples were generated with phyloFlash v3.3b.</p>
Metagenome Assembled Genome for Planticonsortium tenu (FRE)
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Deepurify: a multi-modal deep language model to remove contamination from metagenome-assembled genomes
<p>The SIM2 testing set.</p>
Supporting data for the manuscript "Generation of lineage-resolved complete metagenome-assembled genomes in complex microbial communities"
<p>Supporting data for the manuscript titled "Generation of lineage-resolved complete metagenome-assembled genomes in complex microbial communities". The archive includes:</p> <ul> <li>metaFlye assmeblies and graphs for HiFi and CLR datasets.</li> <li>HiFi and CLR3 bins/MAGs produced using bin3C / DAS_Tool</li> <li>HiFi MAG taxonomy identifications and completeness info</li> <li>MAGPhase results on HiFi and CLR assmeblies </li> <li>Krona plots with sample composition analysis</li> <li>rRNA/tRNA annotations for the HiFi assembly</li> </ul>
Data for "Capturing variation in metagenomic assembly graphs with MetaCortex".
<p>Data for paper "Capturing variation in metagenomic assembly graphs with MetaCortex". Includes all assemblies, simulated reads, and simulated genomes.</p>
Deepurify: a multi-modal deep language model to remove contamination from metagenome-assembled genomes
<p>The SIM1 testing set.</p>
Brown 23 et al - Metagenome Assembled Genomes from Activated Sludge Bioreactors
<p>in this folder are the gtdb classifications, checkm output, and a fasta file for each MAG</p>
Data from: Predicted input of uncultured fungal symbionts to a lichen symbiosis from metagenome-assembled genomes
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Metagenome assembled genomes from mouse gut microbiota
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Metagenome-assembled genomes from two genera of pitcher plants and three freshwater lakes
<p>Illumina shotgun metagenome sequences from <em>Sarracenia </em>and <em>Nepenthes </em>pitcher plants (originally published in Bittleston et al. 2018, MG-RAST RRID: SCR_004814; mgp15454) and three freshwater lakes (Consensus Lake, New York, USA (SRR15064816), Lake Mendota, Wisconsin, USA (SRR11647637), and Lake Samiti, Sikkim, India (SRR10757258)) were binned using CONCOCT v1.1.0 (Alneberg et al. 2014). Bins were further refined using anvi’o’s interactive interface v7.1 (Eren et al. 2015).</p>
ScienceDex guides
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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.