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De novo assembly

Tìm thấy 20+ kết quả cho từ khóa "De novo assembly"

Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations

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Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and. Here we improved the reconstruction of HCMV full genomes by means of a hybrid, de novo genome-assembly bioinformatics pipeline upon data generated from the recently released MinION MkI B sequencer from Oxford Nanopore Technologies..

RNA-Seq analysis of soft rush (Juncus effusus): Transcriptome sequencing, de novo assembly, annotation, and polymorphism identification

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RNA-Seq has been used for other members of the Poales, and particular of members of the family Poaceae, for various purposes such as de novo sequencing and assembly (rice, [49. In this study we carried out both single and paired- end sequencing runs to improve the de novo assembly [57]. The assembly was deemed successful based on a good TransRate score of 0.34 as well BUSCO results that were quite similar to those of the closer relatives S..

Telomere length de novo assembly of all 7 chromosomes and mitogenome sequencing of the model entomopathogenic fungus, Metarhizium brunneum, by means of a novel assembly pipeline

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In this study, we present a novel hybrid assembly pipeline that allowed for both mitogenome de novo assembly and telomere length de novo assembly of all 7 chromosomes of the model entomopathogenic fungus, Metarhizium brunneum.. Full list of author information is available at the end of the article.

Transcriptome profiling of venom gland from wasp species: De novo assembly, functional annotation, and discovery of molecular markers

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Transcriptome profile of the Asian giant hornet (Vespa mandarinia) using illumina HiSeq 4000 sequencing: de novo assembly, functional annotation, and discovery of SSR markers. Occurrence of Hymenoptera (wasps and bees) and their foraging in the southwestern part of Jirisan National Park, South Korea. In: The handbook of environmental chemistry, vol. Structural and functional characterization of two novel peptide toxins isolated from the venom of the social wasp Polybia Paulista.

De novo assembly of Persea americana cv. ‘Hass’ transcriptome during fruit development

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On the other hand, in order to identify candidate genes involved in the development of avocado fruit, we compared samples from and 390 DAFS considering three biological replicates using differential expression analysis. 2 Annotation and relevant GO terms of the de novo transcriptome assembled. The de novo assembly and functional annotation of the avocado transcriptome. In this study we report the de novo assembly of the ‘Hass’.

De novo assembly and comparative transcriptome analysis of Monilinia fructicola, Monilinia laxa and Monilinia fructigena, the causal agents of brown rot on stone fruits

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page=trimmomatic) setting the parameters as follows: i) LEADING and TRAILING = 3, removing bases from the two ends of the reads if below a threshold quality of 3. trinityrnaseq/wiki) was used for the de novo assembly of the transcriptomes using together sequencing data from the six libraries (2 isolates and 3 growing conditions) from each species (Table 1). Default assembly parameters of Trinity were used, with the addition of the “–jaccard_clip”.

The effect of variant interference on de novo assembly for viral deep sequencing

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Effect of variant assembly using popular de novo assemblers.

De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

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Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome. de novo assembly and annotation of the freshwater crayfish Astacus astacus transcriptome

Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis)

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The main objective of the present study is to furnish a genetic resource and a de novo reference genome of mithun to facilitate future research. Our de novo draft assembly is the first genome assembly of Indian mithun, which is constructed using a hybrid approach. This im- proved the overall performance of the genome assembly..

Genomic tools for durum wheat breeding: De novo assembly of Svevo transcriptome and SNP discovery in elite germplasm

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This study presents a de novo transcriptome assembly of Svevo, a modern elite durum wheat cultivar widely used in breeding programs.

A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds

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Long-read sequence assembly of the gorilla genome. The first near- complete assembly of the hexaploid bread wheat genome, Triticum aestivum. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Single- molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus).

Revisiting avian ‘missing’ genes from de novo assembled transcripts

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We demonstrate that de novo assembly of multiple transcriptomes from various tissues can rescue most missing genes in the absence of complete reference genomes, and most pre- sumed missing genes have a strong tissue-specific ex- pression pattern.. De novo transcriptome assembly and quality evaluation The analysis pipeline for discovering ‘missing genes’ is shown in Fig.

The genomes of precision edited cloned calves show no evidence for off-target events or increased de novo mutagenesis

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All pair-wise comparisons of de novo mutation rates reported in this study were conducted using a two- proportions Z-test, and comparisons of de novo muta- tion spectra were conducted using Fisher’s exact test.. GL, ML, RS, DG were involved in supervision of the project. Off-target Effects in CRISPR/Cas9-mediated Genome Engineering. De novo assembly of the cattle reference genome with single-molecule sequencing.

De novo sequencing, assembly and characterisation of Aloe vera transcriptome and analysis of expression profiles of genes related to saponin and anthraquinone metabolism

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Keywords: Aloe vera , Next generation sequencing, Transcriptome, De novo assembly, Secondary metabolism, Differential gene expression. Among all the species, Aloe vera Linne Synonym Aloe barbadensis Miller is considered to be medicinally most potent, therefore, it is most popular [2, 3].

RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

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The majority of the berry fruit species that were used for RNA sequencing and analysis (Table 1) lacked an available reference genome sequence, therefore, de novo assembly of the Illumina reads was carried out for each species using Trinity software. and its BLAST portal [68] were developed to allow mining of the transcriptomic data of the 13 wild and cultivated berry fruit species..

Hybrid genome de novo assembly with methylome analysis of the anaerobic thermophilic subsurface bacterium Thermanaerosceptrum fracticalcis strain DRI-13T

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Conclusions: The de novo hybrid assembly of strain DRI-13 T genome has provided a more contiguous and accurate view of the subsurface bacterium T. fracticalcis, strain DRI-13 T . BMC Genomics https://doi.org/10.1186/s z.

Compacta: A fast contig clustering tool for de novo assembled transcriptomes

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Under this scenario, the best use of information from de novo assembly is formation of a contig cluster that can be used to identify the core set of expressed genes that allows the most effective comparison of the relative ex- pression of such entities based on the design of the RNA-Seq experiment.. Compacta is designed to reduce the number of contigs to a smaller set of representative sequences while pre- serving the information about relative expression given by read abundance.

De novo transcriptome sequencing and analysis of salt-, alkali-, and droughtresponsive genes in Sophora alopecuroides

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De novo characterization of the Anthurium transcriptome and analysis of its digital gene expression under cold stress. De novo assembly of the desert tree Haloxylon ammodendron (C. Landscape of the lipidome and transcriptome under heat stress in Arabidopsis thaliana. Landscape of the lipidome and transcriptome under heat stress inArabidopsis thaliana. Transcriptomic and metabolomic analysis reveals the role of CoA in the salt tolerance of Zygophyllum spp..

Transcriptome analysis of air-breathing land slug, Incilaria fruhstorferi reveals functional insights into growth, immunity, and reproduction

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RNA sequencing, De novo assembly, functional annotation and SSR analysis of the endangered diving beetle, Cybister chinensis. Sequencing and de novo assembly of the Asian clam (Corbicula fluminea) transcriptome using the Illumina GAIIx method. Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon. Transcriptomic analysis of the endangered Neritid species Clithon retropictus:.

Study of spontaneous mutations in the transmission of poplar chloroplast genomes from mother to offspring

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The de novo assembly of each of the 12 read datasets was performed using Minia with five k-mer values of and 59. Time consumption and the quality of the de novo gen- ome assembly are the two most important aspects of the cpDNA assembly. To determine which level of read amount was different from the others, pairwise comparisons of the assembly time among the four read amounts were performed using.