Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
660
datasets available to search
ShareScore release 0.9.0
Dataset results
660 results for “Genome assemblies”
Data from: Genome assembly and annotation of a Drosophila simulans strain from Madagascar
Drosophila simulans is a closely relative of the genetic model D. melanogaster. In an effort to improve the genomic resources for D. simulans, we assembled and annotated the genome of a strain originating from Madagascar (M252), the ancestral range of D. simulans. The comparison of the M252 genome to other available D. simulans assemblies confirmed its high quality, but also highlighted genomic regions that are difficult to assemble with NGS data. The annotation of M252 provides a clear improvement with alternative splicing for 52% of the multiple-exon genes, UTRs for 70% of the genes, 225 novel genes and 781 pseudogenes being reported. We anticipate that the M252 genome will be a valuable resource for many research questions.
Data from: Chromosome-level reference genome assembly and gene editing of the dead-leaf butterfly Kallima inachus
<p class="p">The leaf resemblance of <i><span>Kallima</span></i> (Nymphalidae) butterflies<i> </i>is an important ecological adaptive mechanism that increases survival. However, the genetic mechanism underlying ecological adaptation remains unclear owing to a dearth of genomic information. Herein, we revealed the karyotype (n = 31) of the dead-leaf butterfly <i><span>Kallima inach</span></i><i><span>us</span></i>, assembled its high-quality chromosome-level reference genome (568.92 Mb; contig N50: 19.20 Mb), and identified its Z and candidate W chromosomes. To our knowledge, this is the first study to report on these aspects of this species. In the assembled genome, 15,309 protein-coding genes and 49.86% repeat elements were annotated. Phylogenetic analysis showed that <i><span>K. inachus</span></i> diverged from <i><span>Melitaea cinxia </span></i>(no leaf resemblance), both of which are in Nymphalinae, around 40 million years ago. Demographic analysis indicated that the effective population size of <i><span>K. inach</span></i><i><span>us</span></i> decreased during the last interglacial period in the Pleistocene. The wings of adults with the pigmentary gene <i><span>ebony</span></i> knocked out using CRISPR/Cas9 showed phenotypes in which the orange dorsal region and entire ventral surface darkened, suggesting its vital role in the ecological adaption of dead-leaf butterflies. Our results provide important genome resources for investigating the genetic mechanism underlying protective resemblance in dead-leaf butterflies and insights into the molecular basis of protective coloration.</p>
Data from: "De novo assembled transcriptome of organs involved in reproduction in an endangered endemic Iberian cyprinid fish (Squalius pyrenaicus)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015
Sex determination systems are diverse, especially among fish, and include genetic and/or environmental components. Unexpectedly for such a basic aspect of development, sex determination systems change rapidly during evolution and gonadal fate is not ultimate, being actively maintained lifelong. Here, sequences of expressed genes involved in maintenance of gonad identity and reproduction processes were obtained through transcriptome assembly of the brain-gonadal axis tissues of a freshwater fish inhabiting highly variable environments, the gonochoristic Iberian fish Squalius pyrenaicus. Through Illumina total RNA-sequencing, male and female transcriptomes of brain and gonad tissues were assembled with Trans-ABySS software and merged to produce a more comprehensive S. pyrenaicus transcriptome. Coding sequences (CDS) predicted by TransDecoder were annotated using blastx. By means of read mapping against the reference transcriptome and CDS datasets, using Bowtie2, the accuracy of read mapping was assessed. This first endemic Iberian cyprinid transcriptome of organs involved in reproduction processes may serve as a valuable genomic resource for studying sexual mechanisms and other aspects of evolution, such as speciation and responses to environmental changes, and may be a useful tool for conservation studies since S. pyrenaicus is an endangered species.
Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies
Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate among recent, non-equilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model, and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources.
Data from: Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution
The Heliconius butterflies are a widely studied adaptive radiation of 46 species spread across Central and South America, several of which are known to hybridize in the wild. Here, we present a substantially improved assembly of the Heliconius melpomene genome, developed using novel methods that should be applicable to improving other genome assemblies produced using short read sequencing. First, we whole-genome-sequenced a pedigree to produce a linkage map incorporating 99% of the genome. Second, we incorporated haplotype scaffolds extensively to produce a more complete haploid version of the draft genome. Third, we incorporated ∼20x coverage of Pacific Biosciences sequencing, and scaffolded the haploid genome using an assembly of this long-read sequence. These improvements result in a genome of 795 scaffolds, 275 Mb in length, with an N50 length of 2.1 Mb, an N50 number of 34, and with 99% of the genome placed, and 84% anchored on chromosomes. We use the new genome assembly to confirm that the Heliconius genome underwent 10 chromosome fusions since the split with its sister genus Eueides, over a period of about 6 million yr.
Data from: Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology
The self-incompatible species Arabidopsis halleri is a close relative of the self-compatible model plant Arabidopsis thaliana. The broad European and Asian distribution and heavy metal hyperaccumulation ability make A. halleri a useful model for ecological genomics studies. We used long-insert mate-pair libraries to improve the genome assembly of the A. halleri ssp. gemmifera Tada mine genotype (W302) collected from a site with high contamination by heavy metals in Japan. After five rounds of forced selfing, heterozygosity was reduced to 0.04%, which facilitated subsequent genome assembly. Our assembly now covers 196 Mb or 78% of the estimated genome size and achieved scaffold N50 length of 712 kb. To validate assembly and annotation, we used synteny of A. halleri Tada mine with a previously published high-quality reference assembly of a closely related species, Arabidopsis lyrata. Further validation of the assembly quality comes from synteny and phylogenetic analysis of the HEAVY METAL ATPASE4 (HMA4) and METAL TOLERANCE PROTEIN1 (MTP1) regions using published sequences from European A. halleri for comparison. Three tandemly duplicated copies of HMA4, key gene involved in cadmium and zinc hyperaccumulation, were assembled on a single scaffold. The assembly will enhance the genomewide studies of A. halleri as well as the allopolyploid Arabidopsis kamchatica derived from A. lyrata and A. halleri.
Red clover (Trifolium pratense L.) genome assembly and annotation
<p>De Vega, J. J. <em>et al.</em> Red clover (<em>Trifolium pratense</em> L.) draft genome provides a platform for trait improvement. <em>Sci. Rep.</em> <strong>5</strong>, 17394; doi: 10.1038/srep17394 (2015).</p>
De novo genome assembly of Meloidogyne chitwoodi
<p>A whole genome of <em>M. chitwoodi</em> was <em>de novo</em> assembled by empirically optimizing k-mer sizes </p>
Dataset from "Employing hidden Markov models to assess the genetic content of genome assemblies"
<p>Dataset used to reach the conclusions in "Employing hidden Markov models to assess the genetic content of genome assemblies".</p>
Training sets for small genome assembly with Unicycler in Galaxy
<p>Downsampled datasets for the small genome assembly in Galaxy training. These include 3 files : forward and reverse reads from Illumina sequencing , and Long read file from Oxford Nanopore sequencing.</p>
Chromosome-level genome assembly of Triticum turgidum var 'Kronos'
<p> </p> <h2><strong>This data is made available under the Toronto Agreement. </strong></h2> <p><strong>All of the data listed here is available under the prepublication data sharing principle of the </strong><a href="https://www.nature.com/articles/461168a"><strong>Toronto agreement</strong></a><strong> (1). By using this data, you agree to:</strong></p> <ul> <li><strong>respect the rights of the data producers and contributors to analyze and publish the first global analyses and certain other reserved analyses of this data set in a peer-reviewed publication.</strong></li> <li><strong>not redistribute, release, or otherwise provide access to the data to anyone outside of the group, until the data has been published & submitted to the public data repositories.</strong></li> <li><strong>contact the authors to discuss any plans to publish data or analyses that utilize this data to avoid the overlap of any planned analyses.</strong></li> <li><strong>fully cite the prepublication data along with any applicable versioning details.</strong></li> <li><strong>understand that this data as accessed is precompetitive and is not patentable in its present state.</strong></li> </ul> <p><strong>This agreement does not expire by time but only upon publication of the first global analysis by the data producers and contributors.</strong><br><strong>(1) Toronto International Data Release Workshop Authors. Prepublication data sharing. </strong><em><strong>Nature</strong></em><strong> 461, 168–170 (2009). </strong><a href="https://doi.org/10.1038/461168a"><strong>https://doi.org/10.1038/461168a</strong></a></p> <p> </p> <ul> <li><em>If you have questions about <strong>the use</strong> of this dataset, please contact Ksenia Krasileva: kseniak [at] berkeley.edu</em></li> </ul> <p> </p> <p><strong>Updates in Zenodo v7</strong></p> <p>This update includes annotations of non-coding RNAs. Please refer to our <a href="https://github.com/s-kyungyong/Kronos">github</a> to understand how this datasets were produced. Please check additional datasets here: <a href="https://zenodo.org/records/15801566">Chromosome-level genome assembly of Triticum turgidum var 'Kronos' additional datasets.</a></p> <p> </p> <p><strong>Acknowledgement</strong></p> <p>This work has been funded by the United States Department of Agriculture - National Institute for Food and Agriculture Award (2021-67013-35726). <br><br><br></p>
Test Datasets for iwc workflow VGP5 : Trio Genome Assembly
Open the record for dataset details and reuse information.
Genome Sequence Assembly of Coffea arabica variety Geisha (UCDv1.0)
<p>Genome Sequence Assembly of <i>Coffea arabica</i> variety Geisha (UCDv1.0)</p>
Input and output data and code for PPS2 on 333 vertebrate and111 plant genome assemblies, and for DDS2+ on fungal genome assemblies
<p>The datasets contain PPS2 and DDS2+ source and binary code, other scripts, and some input and output data. Please see the README file after unpacking it. The absolute paths in the scripts need to be modified in order to duplicate the results in this dataset. Most of the input and output data have to be removed from the datasets for quick uploading and downloading; otherwise, the datasets would exceed the 50-Gb size limit.</p>
Test datasets for organelle genome assembly
<p>This is the PacBio HiFi data for the Arabidopsis thaliana organelle genomes extracted from the Darwin Tree of Life (<a href="https://www.darwintreeoflife.org">DToL, https://www.darwintreeoflife.org</a>) project sample ddAraThal4 (<a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJEB51511">https://www.ncbi.nlm.nih.gov/bioproject/PRJEB51511</a>). The data was downsampled to a coverage of ~800x for the chloroplast and ~100x for the mitochondrion.</p>
The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications
<div> <div> <p><a href="https://onlinelibrary.wiley.com/doi/10.1111/age.13181">https://onlinelibrary.wiley.com/doi/10.1111/age.13181</a></p> <h1>The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications</h1> <div> </div> <div> <div> <div> <div><a href="https://onlinelibrary.wiley.com/authored-by/Chen/Jianhai">Jianhai Chen</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Zhong/Jie">Jie Zhong</a>, <a href="https://onlinelibrary.wiley.com/authored-by/He/Xuefei">Xuefei He</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Li/Xiaoyu">Xiaoyu Li</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Ni/Pan">Pan Ni</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Safner/Toni">Toni Safner</a>, <a href="https://onlinelibrary.wiley.com/authored-by/%C5%A0prem/Nikica">Nikica Šprem</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Han/Jianlin">Jianlin Han</a></div> </div> </div> </div> <p>The rapid progress of sequencing technology has greatly facilitated the de novo genome assembly of pig breeds. However, the assembly of the wild boar genome is still lacking, hampering our understanding of chromosomal and genomic evolution during domestication from wild boars into domestic pigs. Here, we sequenced and de novo assembled a European wild boar genome (ASM2165605v1) using the long-range information provided by 10× Linked-Reads sequencing. We achieved a high-quality assembly with contig N50 of 26.09 Mb. Additionally, 1.64% of the contigs (222) with lengths from 107.65 kb to 75.36 Mb covered 90.3% of the total genome size of ASM2165605v1 (~2.5 Gb). Mapping analysis revealed that the contigs can fill 24.73% (93/376) of the gaps present in the orthologous regions of the updated pig reference genome (Sscrofa11.1). We further improved the contigs into chromosome level with a reference-assistant scaffolding method. Using the ‘assembly-to-assembly’ approach, we identified intra-chromosomal large structural variations (SVs, length >1 kb) between ASM2165605v1 and Sscrofa11.1 assemblies. Interestingly, we found that the number of SV events on the X chromosome deviated significantly from the linear models fitting autosomes (<em>R</em><sup>2</sup> > 0.64, <em>p</em> < 0.001). Specifically, deletions and insertions were deficient on the X chromosome by 66.14 and 58.41% respectively, whereas duplications and inversions were excessive on the X chromosome by 71.96 and 107.61% respectively. We further used the large segmental duplications (SDs, >1 kb) events as a proxy to understand the large-scale inter-chromosomal evolution, by resolving parental-derived relationships for SD pairs. We revealed a significant excess of SD movements from the X chromosome to autosomes (<em>p</em> < 0.001), consistent with the expectation of meiotic sex chromosome inactivation. Enrichment analyses indicated that the genes within derived SD copies on autosomes were significantly related to biological processes involving nervous system, lipid biosynthesis and sperm motility (<em>p</em> < 0.01). Together, our analyses of the de novo assembly of ASM2165605v1 provides insight into the SVs between European wild boar and domestic pig, in addition to the ongoing process of meiotic sex chromosome inactivation in driving inter-chromosomal interaction between the sex chromosome and autosomes.</p> </div> </div> <div>The work has been pulished here: https://onlinelibrary.wiley.com/doi/full/10.1111/age.13181</div> <div> </div> <div>The current dataset include the genome annotation files.</div> <div> </div> <div>For the whole-genomic assembly, please check NCBI: </div> <div>https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_021656055.1/</div> <div> <table> <tbody> <tr> <th> </th> <th>GenBank</th> </tr> </tbody> <tbody> <tr> <td>Genome size</td> <td>2.5 Gb</td> </tr> <tr> <td>Total ungapped length</td> <td>2.4 Gb</td> </tr> <tr> <td>Number of scaffolds</td> <td>12,642</td> </tr> <tr> <td>Scaffold N50</td> <td>28.3 Mb</td> </tr> <tr> <td>Scaffold L50</td> <td>25</td> </tr> <tr> <td>Number of contigs</td> <td>41,323</td> </tr> <tr> <td>Contig N50</td> <td>157.9 kb</td> </tr> <tr> <td>Contig L50</td> <td>4,562</td> </tr> <tr> <td>GC percent</td> <td>42</td> </tr> <tr> <td>Genome coverage</td> <td>56.0x</td> </tr> <tr> <td>Assembly level</td> <td>Scaffold</td> </tr> </tbody> </table> <p> </p> <h2>Assembly methods</h2> <div>Sequencing technology 10xgenomics Assembly method Supernova v. 2.1.1 <p> </p> <p>part_** are genome fasta for the GCA_021656055.1</p> <p>You could use the following to combine and uncompress.</p> </div> </div> <div> <div> <div><code><span>cat</span> part_* > archive_combined.zip </code></div> </div> <div> <div> </div> <div><code>unzip archive_combined.zip</code></div> </div> </div> <div> </div> <div> </div>
Galaxy Training Network - Screening assembled genomes for contamination using NCBI FCS
<p>This is a toy dataset generated from an assembled yeast genome (Saccharomyces cerevisiae; GCA_000146045.2) with contaminants added from human, Pseudomonas aeruginosa, and Illumina PCR primers.</p>
Data from: De Novo Genome assembly of the Caucasian dwarf goby Knipowitschia cf. caucasica, a new alien Gobiidae invading the River Rhine
<p><strong>Background (Abstract from Paper)</strong></p> <p>The Caucasian dwarf goby <em>Knipowitschia</em> cf. <em>caucasica</em> is a new invasive alien Gobiidae spreading in the<br>Lower Rhine since 2019. Little is known about the invasion biology of the species and further investiga-<br>tions to reconstruct the invasion history are lacking genomic resources. We assembled a high-quality<br>chromosome-scale reference genome of <em>Knipowitschia</em> cf. <em>caucasica</em> by combining PacBio, Omni-C and<br>Illumina technologies. The size of the assembled genome is 956.58 Mb with a N50 scaffold length of 43 Mb,<br>which includes 92.3 % complete vertebrate/Actinopterygii Benchmarking Universal Single-Copy Orthologs.<br>98.96 % of the assembly sequence was assigned to 23 chromosome-level scaffolds, with a GC-content of<br>42.83 %. Repetitive elements account for 53.08 % of the genome. The chromosome-level genome contained<br>49,622 transcripts with 42,926 multi-exons, of which 45,512 genes were functionally annotated. In summary,<br>the high-quality genome assembly provides a fundamental basis to understand the adaptive advantage of<br>the species.<br><br>The file provided here is the <strong>non-redundant repeat library</strong> (2,812 consensus sequences of repeat families). </p> <p><strong>Method:</strong> Repetitive elements were identified de novo with RepeatModeler version 2.0.1. Repetitive DNA and soft-masking was performed with RepeatMasker version 4.1.1 (Smit et al., 2013) using the repeat library previously identified via RepeatModeler and skipping the bacterial insertion element check (-no_is) and run with rmblastn version 2.10.0+ (Flynn et al., 2020). </p>
A High-quality Genome Assembly of Pseudocydonia sinensis Uncovers Uique Phenylpropanoid Pathways
<p>Filename Description Format<br>Pseudocydonia_sinensis.cds.fasta Coding sequence file, with each entry representing the nucleotide sequence of a gene. FASTA<br>Pseudocydonia_sinensis.prot.fasta Protein sequence file, with each entry corresponding to the amino acid sequence of a transcript. FASTA<br>Pseudocydonia_sinensis.annotation.gff3 Genome feature annotation file, describing the locations of genes, exons, and other genomic features. GFF3<br>Pseudocydonia_sinensis.genome.fasta Genome sequence file, providing the complete nucleotide sequence of the genome. FASTA<br>ARK.pep.fa Protein sequence file containing the deduced ancestral protein sequences for the Rosaceae karyotype. FASTA<br>ARK.gff Simplified GFF file formatted specifically for WGDI toolkit. Contains seven columns: chromosome, gene ID, start, end, strand, order, and gene ID. This file represents the positional and structural information of reconstructed ancestral genes in the Ancestral Rosaceae Karyotype. GFF3(7-columns)</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>
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.