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660 results for “Genome assemblies”
Genome assembly contigs
<p>Assembled genome contigs for a bacteria. </p>
Gene predictions in GFF format for tuatara genome assembly QEPC00000000.1
<p><strong>Maker gene predictions for Sphenodon punctatus (tuatara) isolate: mauimua-1 </strong> <br> <br> These GFF files correspond to the genome assembly in GenBank ID QEPC00000000.1<br> https://www.ncbi.nlm.nih.gov/nuccore/QEPC00000000.1</p> <p>Files:</p> <p> <strong>MASKED_Tuatara.DEVO.annot15102.gff.gz</strong><br> - gene and transcript predictions only<br> <br> <strong>20160427.tuatara.maker.raw.gff3.gz</strong><br> - raw Maker output including gene and transcript predictions, alignment results and output of individual gene prediction algorithms (SNAP and Augustus).</p> <p><br> <br> </p>
Population genetics of Paramecium mitochondrial genomes; genome assemblies and annotation files
<p>Because of issues arising during submission to GenBank of Paramecium mitochondrial genomes due to the highly unconventional nature of the genetic code used in these genomes, we are initially making the genomes publicly available here (while we are still working on a submission to official databases).</p>
Tuatara (Sphenodon punctatus) ab initio interspersed repeat consensus sequences from the Tuatara genome assembly.
<p>These repeat consensus sequences are part of the genome analysis of the Tuatara genome. </p>
Genome assemblies of Bacteroides fragilis CCUG4856T(=ATCC25285=NCTC9343)
<p>Supplementary material for the manuscript <em>Insights from complete, circular genome assembly and plasmid identification of six clinical multidrug resistant Bacteroides fragilis isolates.</em></p> <p>141 genome assemblies of Bacteroides fragilis CCUG4856T(=ATCC25285=NCTC9343) using Illumina and Oxford Nanopore data with the following assemblers and polishing tools</p> <p>Wtdbg2 v2.3 (<a href="https://github.com/ruanjue/wtdbg2">https://github.com/ruanjue/wtdbg2</a>)</p> <p>Miniasm v0.3r179 (<a href="https://github.com/lh3/miniasm">https://github.com/lh3/miniasm</a>)</p> <p>Flye v2.3.7 (<a href="https://github.com/fenderglass/Flye">https://github.com/fenderglass/Flye</a>)</p> <p>Canu v1.8 (<a href="https://github.com/marbl/canu">https://github.com/marbl/canu</a>)</p> <p>Spades (including Hybridspades) v3.13.0 (<a href="https://github.com/ablab/spades">https://github.com/ablab/spades</a>)</p> <p>Skesa v2.3.0 (<a href="https://github.com/ncbi/SKESA">https://github.com/ncbi/SKESA</a>)</p> <p>Unicycler v0.4.7 (<a href="https://github.com/rrwick/Unicycler">https://github.com/rrwick/Unicycler</a>)</p> <p>Nanopolish v0.10.2 (<a href="https://github.com/jts/nanopolish">https://github.com/jts/nanopolish</a>)</p> <p>Racon v1.3.1 (<a href="https://github.com/isovic/racon">https://github.com/isovic/racon</a>)</p> <p>Pilon v1.22 (<a href="https://github.com/broadinstitute/pilon">https://github.com/broadinstitute/pilon</a>)</p> <p> </p> <p>Methods and source code are available in the manuscript and at <a href="https://github.com/thsyd/bfassembly">https://github.com/thsyd/bfassembly</a></p>
States of genome assembly supporting data for complete genome assembly of clinical multidrug resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial resistance genes and plasmids.
<p>Assemblies for each isolate and assembly stage is in .gfa and .fasta format.</p> <p>the best SPAdes assembly is also included in the .zip files.</p> <p>1) Unicycler with illumina data and Nanopore data from the first sequencing run, filtered with FiltLong.<br> 2) Unicycler with illumina data and Nanopore data from the first sequencing run, filtered with FiltLong and error corrected with Canu<br> 3) Unicycler with illumina data and Nanopore data from the first and second sequencing run, filtered with FiltLong.<br> 4) manual finshing of assembly 3. <br> Methods are described in the paper and at the github repository (https://github.com/thsyd/bfassembly)</p> <p> </p>
ST131_4071_genome_assembly_annotation_files_theExtra2
<p>SRR3290149_prokka.gff.gz and ERR1971796_prokka.gff.gz</p>
ST131_4071_genome_assembly_files_part2
<p>ST131_4071_genome_assembly_files_part2</p>
Oenococcus oeni genome assembly - wine CiEs
<p>Genome assembly of three wine-related strains of Oenococcus oeni.</p> <p>New insights into cinnamoyl esterase activity of Oenococcus oeni:</p> <p>Some strains of Oenococcus oeni possess cinnamoyl esterase activity that can be relevant in the<br> malolactic stage of wine production by liberating hydroxycinnamic acids that are precursors of volatile<br> phenol compounds responsible for sensory faults in wine. The objective of this study was to better<br> understand the basis of the differential activity between strains.</p> <p>Remark: The genomes may contain contamination which does not effect the conclusion of the relevant publication about cinnamoyl esterase activity.</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>
Contaminated genome assembly for decontamination training as part of the Galaxy Training Network
Open the record for dataset details and reuse information.
Denovo SPAdes assemblies for isolates included in the 1000-genome panel of Zymoseptoria tritici
<p>SPAdes draft assemblies for isolates included in the 1000-genome panel of <em>Zymoseptoria tritici</em></p> <p> </p> <p>For methods, please refer to: <a href="https://doi.org/10.1038/s41467-023-36674-y"><span>https://doi.org/10.1038/s41467-023-36674-y</span></a></p> <div> <div> </div> </div> <p>Original abstract: </p> <div> <div> <p>Human activity impacts the evolutionary trajectories of many species worldwide. Global trade of agricultural goods contributes to the dispersal of pathogens reshaping their genetic makeup and providing opportunities for virulence gains. Understanding how pathogens surmount control strategies and cope with new climates is crucial to predicting the future impact of crop pathogens. Here, we address this by assembling a global thousand-genome panel of <em>Zymoseptoria tritici</em>, a major fungal pathogen of wheat reported in all production areas worldwide. We identify the global invasion routes and ongoing genetic exchange of the pathogen among wheat-growing regions. We find that the global expansion was accompanied by increased activity of transposable elements and weakened genomic defenses. Finally, we find significant standing variation for adaptation to new climates encountered during the global spread. Our work shows how large population genomic panels enable deep insights into the evolutionary trajectory of a major crop pathogen.</p> </div> </div>
Genome assembly and gene annotations for a Morus alba var. zhenzhubai
Open the record for dataset details and reuse information.
Assemblies generated in the manuscript "Geometric deep learning framework for de novo genome assembly"
<p>Assemblies evaluated in the manuscript "Geometric deep learning framework for de novo genome assembly". All the assemblies were generated by us, except CHM13.ONT.Flye-2.9.fa.gz which was generated by <a href="https://www.nature.com/articles/s41587-019-0072-8">Kolmogorov et al. (2019)</a>.</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>
A chromosome-level genome assembly of the orange wheat blossom midge, Sitodiplosis mosellana Géhin (Diptera: Cecidomyiidae)
<p><span>The Orange wheat blossom midge <i>Sitodiplosis mosellana </i>Géhin (Diptera: Cecidomyiidae), an important insect pest, has caused serious yield losses in most wheat-growing areas worldwide in the past half-century. In this study, we assembled the first chromosomal level genome for <i>S. mosellana</i> using PacBio long-read, Illumina short-read sequences and high-throughput chromatin conformation capture (Hi-C) genome scaffolding techniques. The final genome assembly was 180.69 Mb, with contig and scaffold N50 sizes of 998.71 kb and 44.56 Mb, respectively. Hi-C scaffolding reliably anchored four pseudochromosomes, accounting for 99.67% of the assembled genome. The assembly showed high integrity and quality, with 91.7% of short reads mapped to the genome and a coverage rate of 99.8%. The assembly quality was evaluated using Core Eukaryotic Genes Mapping Approach and Benchmarking Universal Single-Copy Orthologs. In total, 12,269 protein-coding genes were predicted, of which 91% were functionally annotated. Phylogenetic analysis indicated that <i>S. mosellana</i> and its close relative the swede midge <i>Contarinia nasturtii</i> diverged about 32.7 million years ago. <i>S. mosellana</i> genome showed high chromosomal synteny with the genome of <i>Drosophila melanogaster</i> and <i>Anopheles gambiae</i>. The key gene families involved in chemosensation and detoxification of plant secondary chemistry were analysed<i>.</i> The high-quality <i>S. mosellana</i> genome data will provide an invaluable resource for research in a broad range of areas, including the biology, ecology, genetics, and evolution of midges as well as insect-plant interactions and co-evolution, and their relatives more generally.</span></p>
Supporting Data for "Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes"
<p>This dataset contains supporting files referenced by the following publication:</p> <p>• Rabanal FA, Gräff M, Lanz C, Fritschi K, Llaca V, Lang M, Carbonell-Bejerano P, Henderson I, Weigel D. <strong>Pushing the limits of HiFi assemblies reveals centromere diversity between two <em>Arabidopsis thaliana</em> genomes</strong>. <em>Nucleic Acids Research</em>. doi: 10.1093/nar/gkac1115</p> <p> </p> <p>Directory structure:</p> <ul> <li><strong>Bionano_optical_maps_based_assemblies</strong>: this directory contains results from the Bionano optical map based scaffolding for the main long-read assemblers analysed in the study for <em>Arabidopsis thaliana</em> accession Ey15-2 (9994): <ul> <li><strong>9994.CLR_Canu</strong></li> <li><strong>9994.HiFi_FALCON</strong></li> <li><strong>9994.HiFi_HiCanu</strong></li> <li><strong>9994.HiFi_Hifiasm</strong></li> <li><strong>9994.HiFi_IPA</strong></li> <li><strong>9994.HiFi_Peregrine</strong></li> </ul> </li> </ul> <p> </p> <ul> <li><strong>Col-0_HiFi-Hifiasm_assembly</strong>: this directory contains the Pacbio HiFi based chromosome level assembly (fasta file) and repeat annotation (gff file) of <em>Arabidopsis thaliana</em> accession Col-0 (6909). </li> </ul> <p> </p> <ul> <li><strong>Ey15-2_HiFi-Hifiasm_plus_CLR-Canu_assembly</strong>: this directory contains the Pacbio HiFi+CLR based chromosome level assembly (fasta file) and repeat annotation (gff file) of <em>Arabidopsis thaliana</em> accession Ey15-2 (9994). </li> </ul> <p> </p> <ul> <li><strong>Naish2021_Wang2021_repeat_annotation</strong>: this directory contains the repeat annotation (gff files) for the <em>Arabidopsis thaliana</em> Col-0 (6909) assemblies performed by Naish <em>et al.</em> (doi: 10.1126/science.abi7489) and Wang <em>et al.</em> (doi: 10.1016/j.gpb.2021.08.003). </li> </ul> <p> </p> <ul> <li><strong>TAIR10_masked</strong>: this directory contains the repeat-hard-masked version of the TAIR10 <em>Arabidopsis thaliana</em> Col-0 (6909) reference genome that was used for in silico scaffolding of contigs with RagTag (<a href="http://github.com/malonge/RagTag">https://github.com/malonge/RagTag</a>).</li> </ul> <p> </p>
Gaps and complex structurally variant loci in phased genome assemblies
<p>Supplementary data including code for an science article 'Gaps and complex structurally variant loci in phased genome assemblies'.</p>
A chromosome-level genome assembly of Gekko japonicus
<p>We assembled and annotated a chromosome-level genome of <em>Gekko japonicus.</em></p>
Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence
<p>Abstract Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such endogenous viral elements and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of endogenous viral elements. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for 1 generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific endogenous viral elements identified an element comprised of a 9,045-bp stretch of repeated, inverted, and jumbled genome fragments of infectious hypodermal and hematopoietic necrosis virus bounded by a repeated 591/590 bp host sequence. As only near complete linear ∼4 kb infectious hypodermal and hematopoietic necrosis virus genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear endogenous viral element types. The existence of joined inverted infectious hypodermal and hematopoietic necrosis virus genome fragments also provides a means by which hairpin double-stranded RNA could be expressed and processed by the shrimp RNA interference machinery.</p>
ScienceDex guides
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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.