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103 results for “metagenomes assembly”
Orbicella faveolata coral metagenome assemblies from the ECA region of Florida, USA
<p>The enclosed files include <em>Orbicella faveolata</em> coral metagenome assemblies collected from the Coral Ecosystem Conservation Area (ECA) in southeast Florida, USA. Metadata for the files including region of collection and associated NCBI accession numbers is included in this repository as the metadata file. Apparently healthy coral tissue cores were collected between May 28 and June 21, 2021. The DNA was extracted from the host tissue and mucus and sequenced in a paired-end 150 bp format on an Illumina NovaSeq. Trimming and quality filtering of DNA sequences proceeded, followed by host and endosymbiotic dinoflagellate DNA removal. The host-cleaned reads were assembled individually by coral sample into longer contigs using MegaHit v1.1.4. The “Assembly_Fastas” zipped file contains 45 metagenome assemblies from the individual <em>Orbicella faveolata</em> corals. In addition, these metagenome assemblies were annotated with eggnog-mapper v2.1.6 to generate both predicted gene regions and annotation output files. The “Predicted_Gene_Fastas” zipped file contains nucleotide fasta files of the predicted gene regions for the 45 coral metagenome assemblies. The fasta header of each gene includes the contig ID it originated from in the associated “Assembly_Fastas”. The “Predicted_Gene_Annotations” zipped file contains either .csv or .xlsx files with the eggnog-mapper-based annotations. These files contain a “query contig” that corresponds to the contig ID in the fasta header of the “Predicted_Gene_Fastas”. </p> <p>These data were processed and generated by Julie Meyer’s Lab at the University of Florida, using funding from the Florida Department of Environmental Protection.</p>
TOPC_bin_586 metagenome assembled genome (MAG)
<p><strong>Contig, gene sequences and functional annotation of the <em>TOPC_bin_586</em> metagenome assembled genome (MAG)</strong></p> <p>Data available:</p> <ol> <li>Nucleotide sequences of the contigs composing the MAG [<em>topc.bin.586.fna</em>]</li> <li>Amino acid sequences of the genes (open reading frames, ORFs) [<em>topc.bin.586_ORFs.faa</em>]</li> <li>Functional annotation table (tab-delimited) for the ORFs [<em>topc.bin.586_ORFs_annotation.tsv</em>]</li> </ol>
Catalog of metagenome-assembled bacterial genomes from Antarctic endolithic communities
<p>The dataset consists of 2 rar archives and 2 files ( tab-separated values ). Here is a brief summary of their contents:</p> <ul> <li><strong>MAGs_taxonomy: </strong>GTDB classification for each MAG.</li> <li><strong>MAGs_genome_info: </strong>genome size, completeness, contamination, length, N50.</li> <li><strong>MAGs - candidate species: </strong>high quality (HQ) and medium quality (MQ) bacterial metagenome assembled genomes.</li> <li><strong>MAGs_Annotation: </strong>EggNOG annotation files. For each MAG, the following files are included: <ul> <li>eggnog.emapper.annotations: the final EggNOG annotation;</li> <li>eggnog.emapper.hmm_hits: list of significant hits to eggNOG Orthologous Groups</li> <li>eggnog.emapper.seed_orthologs: best match of each query within the best Orthologous Group (OG) reported in the eggnog.emapper.hmm_hits file<strong>.</strong></li> </ul> </li> </ul>
Metagenome assembled genome database of a human cohort and fecal reactors
<p><strong>HumanCohort_annotations.tsv.zip:</strong> This is the custom MAG database (n=2447 MAGs) and corresponding annotations that were used in Borton 2022: "Targeted curation of the gut microbial gene content modulating human cardiovascular disease". The citation will be updated upon publication of the manuscript. Metagenome assembled genomes were generated from fecal metagenomes derived from a 54 person cohort and anoxic methylated amine enrichments. </p> <p><strong>HumanCohortmetabolism_summary.xlsx.zip: </strong> This is the annotation summary for 2447 MAGs in the cohort database. </p> <p><strong>Quality_Abundance_CohortMAGs.xlsx: </strong>This is a genome inventory of the 2447 MAGs in the cohort database including genome statistics and relative abundance. </p> <p><strong>orig_1D_NMR_fids.zip: </strong>NMR data derived from anoxic methylated amine enrichments. </p>
Metagenome-Assembled Genome DRAM Annotations (EMERGE 97% dereplicated MAGs)
<p>This is the combined DRAM annotation outputs for the 1,864 97% dereplicated metagenome-assembled genomes from Stordalen Mire, Sweden. </p> <ul> <li>1864_97percentmags_annotations_combined.tsv.gz</li> <li>1864_97percentmags_metabolism_summary.xlsx</li> <li>product_0.html</li> <li>product_1.html</li> </ul> <p>METHODS:</p> <p>MAGs were annotated and distilled using DRAM (v1.4.0).</p> <p>FUNDING:<br> This research is a contribution of the EMERGE Biology Integration Institute ((https://emerge-bii.github.io/), funded by the National Science Foundation, Biology Integration Institutes Program, Award # 2022070.<br> We thank the Swedish Polar Research Secretariat and SITES for the support of the work done at the Abisko Scientific Research Station. SITES is supported by the Swedish Research Council's grant 4.3-2021-00164.<br> This study was also funded by the Genomic Science Program of the United States Department of Energy Office of Biological and Environmental Research, grant #s DE-SC0004632. DE-SC0010580. and DE-SC0016440.<br> A portion of this research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program (proposal: 10.46936/fics.proj.2017.49950/60006215 and 10.46936/10.25585/60001148) and used resources at the DOE Joint Genome Institute (<a href="https://www.google.com/url?q=https://ror.org/04xm1d337&sa=D&source=docs&ust=1674859614742521&usg=AOvVaw2XgXYw9eI4JIXRMKn3S9Se">https://ror.org/04xm1d337</a>) and the Environmental Molecular Sciences Laboratory (<a href="https://www.google.com/url?q=https://ror.org/04rc0xn13&sa=D&source=docs&ust=1674859614742655&usg=AOvVaw3UXdoHIFmVjc-mXUhDXYQt">https://ror.org/04rc0xn13</a>), which are DOE Office of Science User Facilities operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL).</p>
Novel metagenome assembled genomes (MAGs) that best represent novel species level taxa within the phylum Chloroflexota
<p>1280 Chloroflexita MAGs from the study "Taxonomic re-classification and expansion of the phylum Chloroflexota based on over 5000 genomes and metagenome-assembled genomes". Only MAGs that improved the representation of a species-level genome cluster within the phylum <em>Chloroflexota</em> were included in this deposition.</p> <p>Most of these MAGs were assembled from publicly availabe metagenome sequence data obtained from the NCBI sra database.</p> <p>An overview of the here deposited MAGs can be found in <a href="https://zenodo.org/api/files/2a6a7fa1-489c-426d-8e05-ada23038dfdf/Zenodo_deposited_MAGS_overview.xlsx?versionId=9cde1488-8388-4fdb-a45e-2d48dc066f9a"> Zenodo_deposited_MAGS_overview.xlsx</a>, for more details please refer to the abive mentioned publication.</p> <p>MAG assemblies are deposited as gzip compressed tar.archive. Three tar.gz archives have been deposited, containing the same MAG assemblies but sorted by different criteria:</p> <ol> <li>All MAGs sorted by category of the source environment</li> <li>All MAGs sorted by class designation</li> <li>All MAGs sorted by MIMAG quality (high or moderate)</li> </ol>
Metagenome-assembled genomes(MAGs) generated by MetaCC binning
<p>MAGs generated by MetaCC binning from the human gut short-read, the wastewater (WW) short-read, the cow rumen long-read, and the sheep gut long-read metaHi-C datasets</p>
The LakePulse Metagenome-Assembled Genome catalogue
<p>Lakes are heterogenous ecosystems inhabited by a rich microbiome whose genomic diversity is poorly defined. We present a continental-scale study of metagenomes representing 6.5-million km<sup>2</sup> of the most lake-rich landscape on Earth. Analysis of 308 Canadian lakes resulted in a metagenome-assembled genome (MAG) catalogue of 1,008 mostly novel bacterial genomospecies. Lake trophic state was a leading driver of taxonomic and functional diversity among MAG assemblages, reflecting the responses of communities profiled by 16S rRNA amplicons and gene-centric metagenomics. Coupling the MAG catalogue with watershed geomatics revealed terrestrial influences of soils and land use on assemblages. Agriculture and human population density were drivers of turnover, indicating detectable anthropogenic imprints on lake bacteria at the continental scale. The sensitivity of bacterial assemblages to human impact reinforces lakes as sentinels of environmental change. Overall, the LakePulse MAG catalogue greatly expands the freshwater genomic landscape, advancing an integrative view of diversity across Earth's microbiomes.</p>
The LakePulse Metagenome-Assembled Genome catalogue
Open the record for dataset details and reuse information.
Supplementary data (simulated metagenome set 2) 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 closely related Bacteorides strains.</p> <p>The phyloFlash software is available from https://github.com/HRGV/phyloFlash. Examples were generated with phyloFlash v3.3b.</p>
Supplementary data (simulated metagenome set 3) 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 closely related Bacteorides strains.</p> <p>The phyloFlash software is available from https://github.com/HRGV/phyloFlash. Examples were generated with phyloFlash v3.3b.</p>
Antarctic endolithic bacterial metagenome-assembled genomes
<p>Bacterial assembled genomes and annotation data from the Antarctic cryptoendolithic communities collected during the XXXI (2015-16) Italian Antarctic Expedition.</p> <p>The dataset consists of 4 zip archives and 3 files (comma-separated values). Here is a brief summary of their contents:</p> <ul> <li><strong>MAGs: </strong>high quality (HQ) and medium quality (MQ) bacterial metagenome assembled genomes.</li> <li><strong>MAGs_metadata: </strong>completeness, contamination, length, N50, GTDB classification for each MAG.</li> <li><strong>MAGs_HQ_CDS:</strong> translated coding sequences for each high quality MAG.</li> <li><strong>MAGs_HQ_Annotation: </strong>EggNOG annotation files. For each high quality MAG, the following files are included: <ul> <li>eggnog.emapper.annotations: the final EggNOG annotation;</li> <li>eggnog.emapper.hmm_hits: list of significant hits to eggNOG Orthologous Groups</li> <li>eggnog.emapper.seed_orthologs: best match of each query within the best Orthologous Group (OG) reported in the eggnog.emapper.hmm_hits file<strong>.</strong></li> </ul> </li> <li><strong>Jiangella_Antarctica: </strong><em>Candidatus Jiangella antarctica</em> representative genome (UniValnordMG_2_bin.36.fa) and the extracted ribosomal RNA genes (rRNA.fasta).</li> <li><strong>Order_MSA: </strong>protein multiple sequence alignments using the 120 GTDB bacterial marker genes. These alignments were used to estimate divergence times on orders containing at least 4 CBS, for a total of 19 orders.</li> <li><strong>Samples_accession</strong>: table that relates to the NCBI deposition of the shotgun metagenomes, the following info are included: <ul> <li>NCBI Sequence Read Archive (SRA)</li> <li>BioProject accession numbers</li> <li>JGI Integrated Microbial Genomes & Microbiomes site IDs</li> <li>N50 values</li> <li>Metadata</li> </ul> </li> <li><strong>Samples_metadata: </strong>geographic coordinates, temperature, relative humidity and sampling date are reported.</li> </ul>
High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes
<p>This project contains anvi'o profiles and contigs databases that is used and/or referenced from the Lee STM and Khan SA, <em>et al.</em> study titled "<strong>High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes</strong>". The pre-print of this study is available via http://dx.doi.org/10.1101/090993.</p> <p>To be able to work with the data files you will need anvi'o <strong>v2.1.0</strong> to be installed on your system. For installation instructions, or to have access to a Docker image for anvi'o, please visit this URL: http://merenlab.org/software/anvio</p> <p>Public data:</p> <ul> <li><strong>ANVIO-FMT-D-R01-R02-QUICK-VISUALIZATION.tar.gz</strong>: Data files for a quick visualization of the 97 MAGs and their distribution across the two FMT recipients. A run script in the archive explains how to use this data.<br> </li> <li><strong>ANVIO-FMT-D-R01-R02-MERGED-PROFILE.tar.gz</strong>: The merged anvi'o profile for the entire data, which also contains a collection of 97 MAGs identified in the donor. The profile database contains no hierarchical clustering of contigs, however, individual MAGs can be displayed via the following notation since the collection 'MAGs' describe the organization of contigs in each MAG referenced from the dataset `ANVIO-FMT-D-R01-R02-QUICK-VISUALIZATION`, as well as from the paper: "anvi-refine -c CONTIGS.db -p PROFILE.db -C MAGs -b <em>FMT-Donor_MAG_00054</em>". All MAG names are in the supplementary tables in our paper.<br> </li> <li><strong>ANVIO-FMT-D-R01-R02-MAGs-SUMMARY.tar.gz</strong>: A static HTML website that contains FASTA files for each MAG, and TAB-delimited matrices for coverage and detection values, and others. After unpacking, you can double-click the index.html file. </li> </ul>
Non-redundant metagenome-assembled genomes of activated sludge reactors at different disturbances and scales
<p>Metagenome-assembled genomes (MAGs) are microbial genomes reconstructed from metagenomic data and can be assigned to known taxa or lead to uncovering novel ones. MAGs can provide insights into how microbes interact with the environment. Here, we performed genome-resolved metagenomics on sequencing data from four studies using sequencing batch reactors at microcosm (~25 mL) and mesocosm (~4 L) scales inoculated with sludge from full-scale wastewater treatment plants. These studies investigated how microbial communities in such plants respond to two environmental disturbances: the presence of toxic 3-chloroaniline and changes in organic loading rate. We report 839 non-redundant MAGs with at least 50% completeness and 10% contamination (MIMAG medium-quality criteria). From these, 399 are of putative high-quality, while sixty-seven meet the MIMAG high-quality criteria. MAGs in this catalogue represent the microbial communities in sixty-eight laboratory-scale reactors used for the disturbance experiments, and in the full-scale wastewater treatment plant which provided the source sludge. This dataset can aid meta-studies aimed at understanding the responses of microbial communities to disturbances, particularly as ecosystems confront rapid environmental changes.</p>
Metagenome-Assembled Genomes of 2_2_Ac_Mat
<p>The dataset is featured in the data report titled "MAGnificent Microbes: Metagenome-Assembled Genomes of Marine Microorganisms in Mats from a Submarine Groundwater Discharge Site in Mabini, Batangas, Philippines." The study utilized shotgun metagenomics to examine the diversity and functional profiles of marine microorganisms in microbial mats from an SGD-influenced site in Mabini. The dataset includes extracted metagenome-assembled genomes (MAGs) along with their annotations using RAST.</p>
Zostera marina leaf associated bacterial metagenome assembled genomes
<p>Metagenome assembled genomes (MAGs) associated with:</p> <p>A genomic resource for exploring bacterial-viral dynamics in seagrass ecosystems</p> <p>Analysis, code, intermediate and supporting files are archived here: <a href="https://doi.org/10.5281/zenodo.14226514">10.5281/zenodo.14226514</a></p> <p>Viral sequences from this work are archived here: <a href="https://doi.org/10.5281/zenodo.14226038">10.5281/zenodo.14226038</a><br><br>This archive contains:<br>(i) Fifty-six fasta files representing the MAGs described in the above titled work with > 80% completion and < 10% contamination based on CheckM2 metrics<br>(ii) Metadata file describing the MAGs (i.e., subset of Table S3 from the above work)</p>
Metagenome-assembled genomes(MAGs) generated from soil dataset.
<p>MAGs generated from soil dataset 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>
Twenty-five metagenome assembled genomes recovered from the gut microbiome of the domestic ferret, Mustela putorius
<p>This dataset is composed of 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 in the American Society for Microbiology Resource Announcement by Amundson et al. (in prep). </p>
HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota.
<p>We reported 102 complete metagenome assembled genomes (cMAGs) from five human fecal HiFi sequencing samples.</p> <p>102_cMAGs_fna.tar.gz: Fasta sequence files of 102 cMAGs.</p> <p>gc_skew_figures.tar.gz: GC-skew pattern figures of 102 cMAGs. (SVG format)</p> <p>coverage_plots.tar.gz: Genome coverage plot of 102 cMAGs.</p>
Dereplicated Metagenome assembled genomes (MAGs) from Columbia River hyporheic sediments
<p>Fasta file containing 55 metagenome assembled genomes (MAGs) from publication to be submitted titled "<strong>Microbial genome-resolved metaproteomic analyses frame intertwined carbon and nitrogen cycles in river hyporheic sediments". </strong></p>
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Allen Brain Atlas
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International Brain Laboratory public data
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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.