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660 results for “Genome assemblies”
A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus
<p><span>Despite increasing sequencing efforts, numerous fish families still lack a reference genome, which complicates genetic research. One such understudied family is the sand lances (Ammodytidae, literally: 'sand burrower'), a globally distributed clade of over 30 fish species that tend to avoid tidal currents by burrowing into the sand. Here, we present the first annotated chromosome-level genome assembly of the great sand eel (<em>Hyperoplus</em> <em>lanceolatus</em>). The genome assembly was generated using Oxford Nanopore Technologies long sequencing reads and Illumina short reads for polishing. The final assembly has a total length of 808.5 Mbp, of which 97.1% were anchored into 24 chromosome-scale scaffolds using proximity-ligation scaffolding. The assembly is highly contiguous with a scaffold and contig N50 of 33.7 Mbp and 31.3 Mbp, respectively, and has a BUSCO completeness score of 96.9%. The presented genome assembly is a valuable resource for future studies of sand lances, as they are of great ecological and commercial importance and may also contribute to studies aiming to resolve the suprafamiliar taxonomy of bony fishes.</span></p>
Genome annotation associated with the publication "Chromosome-level genome assembly of the Cape cliff lizard (Hemicordylus capensis)"
<p>Genome annotation associated with the publication "Chromosome-level genome assembly of the Cape cliff lizard (<em>Hemicordylus capensis</em>)"</p> <p>rHemCap1.1.gff3 - Genome annotation in GFF3 format<br> rHemCap1.1.proteins.fa - Multi-fasta file of protein coding genes<br> rHemCap1.1.cds-transcripts.fa - Multi-fasta file of transcripts (CDS)</p> <p> </p>
Genome assembly and annotation files of Colletotrichum graminicola strain TZ-3
<p>The maize anthracnose stalk rot and leaf blight diseases caused by the fungal pathogen Colletotrichum graminicola is emerging as an important threat to corn production worldwide. In this work, we provide an improved genome assembly of C. graminicola strain TZ-3 by using the PacBio Sequel II and Illumina high-throughput sequencing technologies. We hope that this genome information will facilitate the pathogenesis research of this plant pathogen.</p>
Draft genome assembly of the alpine carnation Dianthus sylvestris (Caryophyllaceae)
<p>A draft reference sequence for the alpine carnation <em>Dianthus sylvestris</em> was obtained using a combination of paired-end and mate-pair Illumina libraries implemented in the Allpath-LG assembler. The initial assembly was improved through nucleotide correction, gap filling and the assessment of misassemblies, and subsequently annotated with the support of RNA-seq data through the Maker2 pipeline. The final assembly consists of ~440 MB in ~21 K scaffolds (N50 ~61 Kb) covering 86% of Busco eukaryotic genes and ~73% of the estimated genome size (600 Mb). Structural annotation includes ~22 K predicted genes (N50 ~1.8 Kb). </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>
Date for: The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into melanic pigmentation of anemonefish
<p><span>Anemonefish are an emerging group of model organisms due to interesting biological traits such as sequential hermaphroditism, social control of size, symbiosis with anemones, and varying pigmentation patterns. In addition to genus-specific traits, the anemonefish <em>Amphiprion</em> <em>clarkii</em> possesses species-specific characteristics such as interspecies co-habitation, high intraspecies color variation, no anemone specificity, and a broad distribution, that have the potential to further our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. However, despite its position as an emerging model species, the genome of <em>A. clarkii </em>is yet to be published. Here, using PacBio long-read, Illumina short-read and Hi-C chromatin capture technology we generated a high-quality chromosome-scale genome for the anemonefish <em>A. clarkii</em>. The initial assembly consisted of 1840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and then annotated with 25,050 </span>protein-coding gene models. With the chromosome-scale assembly encompassing 98.7% of conserved actinopterygian genes and the annotation containing 97.0%, the quality and completeness of this <em>A. clarkii</em> genome is the highest amongst all published anemonefish genomes. The publication of this high-quality genome, along with <em>A. clarkii'</em>s many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.</p>
Inversion polymorphism in a complete human genome assembly
<p>Supplementary data including code for an journal article titled 'Inversion polymorphism in a complete human genome assembly'.</p>
Virgin Birth: A genetic basis for facultative parthenogenesis in Drosophila - genome assemblies
<p>Drosophila mercatorum genome assemblies used in https://doi.org/10.1101/2022.03.13.484157.</p> <p>The wildtype assembly is non-parthenogenic, while the "partho" assembly is parthenogenic.</p> <p>Assembly process is described here: https://github.com/ekg/drosophila.</p>
Genome sequences for 2031 Saccharomyces cerevisiae genome assemblies
<p>Genome sequences for 2031 Saccharomyces cerevisiae genome assemblies</p>
Detailed information for 2032 Saccharomyces cerevisiae genome assemblies
<p>Detailed information for 2032 Saccharomyces cerevisiae genome assemblies</p>
Gene sequences for 2031 Saccharomyces cerevisiae genome assemblies
<p>Gene sequences for 2031 Saccharomyces cerevisiae genome assemblies</p>
Gene coordinates for 2031 Saccharomyces cerevisiae genome assemblies
<p>Gene coordinates for 2031 Saccharomyces cerevisiae genome assemblies</p>
Protein sequences for 2031 Saccharomyces cerevisiae genome assemblies
<p>Protein sequences for 2031 Saccharomyces cerevisiae genome assemblies</p>
Predicted protein functions for 2031 Saccharomyces cerevisiae genome assemblies
<p>Predicted protein functions for 2031 Saccharomyces cerevisiae genome assemblies</p>
Assembly and annotation of the saguaro cactus genome – SGP5p v2
<p class="MsoNormal">We present an improved genome assembly of the saguaro cactus (<em>Carnegiea gigantea</em> (Engelm.) Britton & Rose), obtained by incorporating long-read PacBio data to the existing short reads. The assembly improves in terms of total size, contiguity, and accuracy, allowing us to extend the range of sequence analyses beyond the single-gene scale. Consequently, 20% more genes were identified, expanding the resources for a neglected yet very peculiar plant family such as Cactaceae.</p>
Metagenome Assembly Genome Bins.tar
<p>Metagenome assembly genome bins of cattle</p>
A high-quality genome assembly for Dillenia turbinata (Dilleniales)
<p class="MsoNormal">Objectives<span>: </span><br><em>Dillenia turbinata</em> (Dilleniaceae) is a member of the order Dilleniales, an enigmatic clade of critical importance for understanding the diversification history of flowering plants but for which genome sequences are not available. We have produced and annotated a chromosome-scale whole genome assembly for <em>D. turbinata</em> through the resources of the 10KP (10,000 Plants) Genomes Project. The genome assembly and associated data provided here will serve as a useful resource for comparative and evolutionary genomics research across the flowering plants.</p> <p class="MsoNormal">Data description: <br>The <em>D. turbinata</em> genome was assembled from Oxford Nanopore Technology (ONT) and whole-genome shotgun (WGS) sequences, and scaffolded into chromosome-scale pseudomolecules using Hi-C data. The genome assembly is 723,739,077 base pairs in length with a BUSCO completeness score of 97%. Twenty-eight scaffolds contain more than 99% of the assembly. The repeat-masked genome sequence is annotated with 36,967 protein-coding gene models (93% BUSCO completeness) supported by transcriptome/protein evidence and/or Pfam domain content. These measures indicate high contiguity and completeness for the <em><span>D. turbinata</span></em> genome.</p>
Repeat annotation of a chromosomal-level assembly of the Callosobruchus maculatus genome
<p>A curated repeat library <c.mac_HiC_plus_beetle_library.lib> was constructed by manually curating the most abundant interspersed repeats identified using RepeatModeler (Smit et al., 2010). The curated library was combined with a beetle-specific library, constructed using RepeatMasker’s queryRepeatDatabase.pl script (-species coleoptera). The genome repeat annotation was generated with RepeatMasker (Smit and Hubley, 2010).</p>
Chromosome-level Genome Assembly of Euphorbia peplus
<p>Code used in genome assembly and annotation: https://github.com/ariellerjohnson/Euphorbia-peplus-genome-project Raw data is available in NCBI PRJNA837952 Euphorbia peplus Genome sequencing and assembly. Also check out our interactive genome browser: https://euphorbgenomes.biohpc.cornell.edu/ And our interactive expression browser: https://bar.utoronto.ca/efp_euphorbia/cgi-bin/efpWeb.cgi</p>
High-resolution KIR allele annotations for HPRC 47 assemblies and other reference genomes using SKIRT
<p><strong>Leveraging the high-quality genome assemblies from the Human Pangenome Reference Consortium (HPRC), we present a novel bioinformatic tool, the Structural KIR annoTator (SKIRT), to annotate, identify, and discover hundreds of novel alleles, more than a dozen structural variations among KIR genes, and all haplotypes carrying novel alleles, confirming KIR genetic diversity. The use of HPRC data needs to comply with the rules announced by HPRC.</strong></p>
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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.