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53 results for “Genome sequence assembly”
A Simulated Heterozygous Diploid Genome for Third-gen Sequencing, Assembly, and Curation
<p>A simulated heterozygous diploid genome based on <em>Saccharomyces</em> <em>cerevisiae</em>, and <em>S. paradoxus</em> homologous chromosomes.</p> <p>Simulated PacBio subreads were generated from both parent haplomes and mixed together. A phased assembly was produced using FALCON assembler and FALCON Unzip (doi:10.1038/nmeth.4035). This dataset and assembly were then used to validate the Purge Haplotigs pipeline (https://bitbucket.org/mroachawri/purge_haplotigs). See workflow.sh for commands, comments and file descriptions.</p>
apomixis_parallel_evolution, and Fortunella hindsii (Citrus hindsii )Genome sequencing and assembly
<p>##The assemble(genome) files</p> <p>Citrus hindsii (Mini citrus)Genome assembly</p> <p>Citrus hindsii (Mini citrus)Genome assembly gene model gff3 file</p> <p>Citrus hindsii (Mini citrus)Genome assembly function annotation</p> <p>Citrus hindsii (Mini citrus)Genome assembly TE gff3 file</p> <p>##The population dataset</p> <p>LD_pur.vcf.gz //The LD purning SNP vcfs (1.4 M sites) used in analysis</p> <p><br> log10_auxin.txt //The expression (log10) related to auxin pathway</p> <p><br> sjg.temergedref.fasta.gz //The TE insertion modify genome in popTE2 analysis</p> <p><br> SVs.vcf.gz //The SV vcfs used in the paper</p> <p><br> te-hierarchy.txt //The TE classfication in popTE2 analysis</p> <p><br> TPM_count.txt //All samples expression in TMP count</p> <p><br> unfiltered.vcf.gz //The unfiltered vcfs file (7.3 M sites, within 0.4 M indels) </p>
Genome annotations of Drosophila melanogaster and Drosophila simulans wild-type strains from long read sequencing assemblies
<p>Genome assemblies were performed for eight wild-type strains of Drosophila melanogaster and Drosophila simulans from Oxford Nanopore long read sequencing (please refer to Mohamed et al. Cells 2020 (doi:10.3390/cells9081776)). Assemblies were deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB50024 (<a href="https://www.ebi.ac.uk/ena/browser/view/PRJEBxxxx">https://www.ebi.ac.uk/ena/browser/view/</a>PRJEB50024).</p> <p>Transposable Element annotations: we used RepeatMasker 4.1.0 (<a href="http://repeatmasker.org/">http://repeatmasker.org/</a>) -species Drosophila, followed by OneCodeToFindThemAll (Bailly-Bechet et al. 2014) with default parameters.</p> <p>Gene annotations: We retrieved gtf files from FlyBase : <a>ftp.flybase.net/genomes/D</a><a>rosophila_melanogaster/dmel_r6,46_FB2022_03/gft/dmel-all-r6.46.gtf.gz</a> and <a>ftp.flybase.net/genomes/Drosophila_simulans/dsim_r2,02_FB2017_04/gtf/dsim-all-</a><a>r2,02.gtf.gz</a>. The corresponding fasta files were also downloaded from FlyBase: <a>ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6,46_FB2022_03/</a><a>fasta</a><a>/dmel-all-</a><a>chromosome-</a><a>r6.46.</a><a>fasta</a><a>.gz</a> and <a>ftp.flybase.net/genomes/Drosophila_simulans/dsim_r2,02_FB2017_04/</a><a>fasta</a><a>/dsim-all-</a><a>chromosome-</a><a>r2,02.</a><a>fasta</a><a>.gz</a>. We used Liftoff (Shumate and Salzberg, 2020) to lift over gene annotations from the references to our genome assemblies. We used -flank 0.2 and only kept the “gene” and “exon” terms.</p>
Adapter sequences used for trimming of genomic sequences in the assembly of the Northern Spotted Owl (<i>Strix occidentalis caurina</i>) genome assembly version 1.0
<p>These files provide the sequences of the adapters used in the construction of the genomic libraries Hanna et al. (2017a) sequenced and used to assemble the Northern Spotted Owl (<em>Strix occidentalis caurina</em>) genome assembly version 1.0 (Hanna et al. 2017b). These files also contain relevant supplemental adapter sequences from the adapter files included with Trimmomatic version 0.36 (Bolger, Lohse & Usadel, 2014).</p> <p><strong>SRR4011595_adapters.fa</strong> : This FASTA format file contains the full length sequences of the adapters Hanna et al. (2017a) used to construct the genomic library they sequenced to produced the data uploaded as NCBI Sequence Read Archive (SRA) run accession SRR4011595. I have also included the partial adapter sequences provided in the "TruSeq3-PE-2.fa" and "NexteraPE-PE.fa" files distributed with Trimmomatic version 0.36 (Bolger, Lohse & Usadel, 2014).</p> <p><strong>SRR4011596_adapters.fa</strong> : This FASTA format file contains the full length sequences of the adapters Hanna et al. (2017a) used to construct the genomic library they sequenced to produced the data uploaded as NCBI Sequence Read Archive (SRA) run accession SRR4011596. I have also included the partial adapter sequences provided in the "TruSeq3-PE-2.fa" and "NexteraPE-PE.fa" files distributed with Trimmomatic version 0.36 (Bolger, Lohse & Usadel, 2014).</p> <p><strong>SRR4011597_adapters.fa</strong> : This FASTA format file contains the full length sequences of the adapters Hanna et al. (2017a) used to construct the genomic library they sequenced to produced the data uploaded as NCBI Sequence Read Archive (SRA) run accession SRR4011597. I have also included the partial adapter sequences provided in the "TruSeq3-PE-2.fa" and "NexteraPE-PE.fa" files distributed with Trimmomatic version 0.36 (Bolger, Lohse & Usadel, 2014).</p> <p><strong>SRR4011614_adapters.fa</strong> : This FASTA format file contains the full length sequences of the adapters Hanna et al. (2017a) used to construct the genomic library they sequenced to produced the data uploaded as NCBI Sequence Read Archive (SRA) run accession SRR4011614. I have also included the partial adapter sequences provided in the "TruSeq3-PE-2.fa" and "NexteraPE-PE.fa" files distributed with Trimmomatic version 0.36 (Bolger, Lohse & Usadel, 2014).</p> <p><strong>SRR4011615_adapters.fa</strong> : This FASTA format file contains the full length sequences of the adapters Hanna et al. (2017a) used to construct the genomic library they sequenced to produced the data uploaded as NCBI Sequence Read Archive (SRA) run accession SRR4011615. I have also included the partial adapter sequences provided in the "TruSeq3-PE-2.fa" file distributed with Trimmomatic version 0.36 (Bolger, Lohse & Usadel, 2014).</p> <p><strong>SRR4011616_adapters.fa</strong> : This FASTA format file contains the full length sequences of the adapters Hanna et al. (2017a) used to construct the genomic library they sequenced to produced the data uploaded as NCBI Sequence Read Archive (SRA) run accession SRR4011616. I have also included the partial adapter sequences provided in the "TruSeq3-PE-2.fa" file distributed with Trimmomatic version 0.36 (Bolger, Lohse & Usadel, 2014).<br> <br> <strong>SRR4011617_adapters.fa</strong> : This FASTA format file contains the full length sequences of the adapters Hanna et al. (2017a) used to construct the genomic library they sequenced to produced the data uploaded as NCBI Sequence Read Archive (SRA) run accession SRR4011617. I have also included the partial adapter sequences provided in the "TruSeq3-PE-2.fa" file distributed with Trimmomatic version 0.36 (Bolger, Lohse & Usadel, 2014).</p>
Draft genome assemblies of killifish from the Fundulus genus with ONT and Illumina sequencing platforms
<p>Four species from the genus Fundulus were selected for genome sequencing to study the physiological and genetic mechanisms that diverge between euryhaline and stenohaline freshwater species within this cyprinodontiform order of ray-finned fishes.</p>
Genome sequencing and assembly of Lathyrus sativus
<p>The dataset contains the whole-genome assembly and protein sequences of <em>Lathyrus sativus</em> cultivar Pusa-24.</p>
Data from: Improved genome assembly of the whiteleg shrimp Penaeus (Litopenaeus) vannamei using long- and short-read sequences from public databases
Open the record for dataset details and reuse information.
MarkerScan: Separation and assembly of cobionts sequenced alongside target species in biodiversity genomics projects
<p>This dataset represents all results files described in the paper 'MarkerScan: Separation and assembly of cobionts sequenced alongside target species in biodiversity genomics projects'.</p>
A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies
<p>The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non-model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast-evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy-number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno-Polymorphism Database (IPD-MHC), a curated resource intended to aid in the systematic compilation of MHC alleles across several species, to support conservation initiatives.</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>
179 high quality metagenome-assembled genomes sequences and annotations
<p>We analyzed seven sediment samples collected adjacent to ferromanganese nodules from the Clarion–Clipperton Fracture Zone (CCFZ) in the eastern Pacific Ocean. Through deep metagenomic sequencing, assembly, and binning, we reconstructed 179 high quality metagenome-assembled genomes (MAGs). This archive contains these genomes sequences and annotations. </p>
PacBio whole-genome sequencing and draft assembly of Stentor coeruleus
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Three haplotype-resolved pentaploid Rosa assemblies with assembled and extracted single copy orthologue (SCO) sequences from Rosa canina genome, diploid Rosa species, and sect. Caninae pollen
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Genome sequence assembly and annotation of MATA and MATB strains of <em>Yarrowia lipolytica</em>
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A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies
Open the record for dataset details and reuse information.
Data from: Chromosome-level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of Nanopore Sequencing, Bionano and Hi-C technology
<p><i>Onychostoma macrolepis</i> is an emerging commercial cyprinid fish species. It is a model system for studies of sexual dimorphism and genome evolution. Here, we report the chromosome-level assembly of the<i> O.macrolepis</i> genome obtained from the integration of Nanopore long-read sequencing with physical maps produced using Bionano and Hi-C technology. A total of 87.9 Gb of Nanopore sequence provided approximately 100-fold coverage of the genome. The preliminary genome assembly was 883.2 Mb in size with a contig N50 size of 11.2 Mb. The 969 corrected contigs obtained from Bionano optical mapping were assembled into 853 scaffolds and produced an assembly of 886.5 Mb with a scaffold N50 of 16.5 Mb. Finally, using the Hi-C data, 881.3 Mb (99.4% of genome) in 526 scaffolds were anchored and oriented in 25 chromosomes ranging in size from 25.27 to 56.49 Mb. In total, 24,770 protein-coding genes were predicted in the genome, and ~96.85% of the genes were functionally annotated. The annotated assembly contains 93.3% complete genes from the BUSCO reference set. In addition, we identified 409 Mb (46.23% of the genome) of repetitive sequence, and 11,213 non-coding RNAs, in the genome. Evolutionary analysis revealed that <i>O.macrolepis</i> diverged from common carp approximately 24.25 million years ago. The chromosomes of <i>O.macrolepis</i> showed an unambiguous correspondence to the chromosomes of zebrafish. The high-quality genome assembled in this work provides a valuable genomic resource for further biological and evolutionary studies of <i>O. macrolepis</i>.</p>
Genome Sequence Assembly of Coffea arabica variety Geisha (UCDv1.0)
<p>Genome Sequence Assembly of <i>Coffea arabica</i> variety Geisha (UCDv1.0)</p>
Xcc BrA1 re-sequenced genome contigs, annotation file and Trinitiy De-nove assembled DEG's
<p>Assembled genome contigs of Xcc strain BrA1 (Behlau et al 2017) which was re-sequenced by our lab and used in a copper stress Transcriptome study. A hybrid RNA-seq analysis pipeline was used and the DEG Trinity De-novo assembled transcripts are also included.</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 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>
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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.