de novo transcriptome assembly
Improved Annotation with de novo Transcriptome Assembly in Four Social Amoeba Species
... robust de novo RNA-seq assembly 605 across the dynamic range of expression ...SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq ...
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Exploiting orthology and de novo transcriptome assembly to refine target sequence information
... sequences. Transcriptome analysis by RNA-Seq has been established as a standard method for gene expression ...via de novo transcriptome ...
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Bridger: a new framework for de novo transcriptome assembly using RNA seq data
... for de novo transcriptome assembly by introducing an auxiliary graph, without the help of any genomic in- ...all de novo assemblers, and even comparable to the reference-based ...
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IsoTree: A New Framework for De novo Transcriptome Assembly from RNA-seq Reads
... for De novo Transcriptome Assembly from RNA-seq Reads Jin Zhao, Haodi Feng*, Daming Zhu, Chi Zhang, and Ying Xu Abstract—High-throughput sequencing of mRNA has made the deep and efficient ...
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SSP: An interval integer linear programming for de novo transcriptome assembly and isoform discovery of RNA-seq reads
... of de novo transcriptome assembly is assembling reads into unique contiguous ...use de novo genome ...other de novo genome assemblers, is to use the redundancy of ...
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Clustering of Short Read Sequences for de novo Transcriptome Assembly
... of transcriptome analysis in various biological studies and considering the vast amount of whole transcriptome sequencing data, it seems necessary to develop an algorithm to assemble transcriptome ...
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De Novo Transcriptome Assembly For The Tropical Grass Panicum Maximum Jacq.
... species) and dicots (1,200 species). The importance of C 4 plants arises mainly from their global primary productivity; they account for approximately a quarter of total production [10]. In addition to their benefits for ...
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A consensus approach to vertebrate de novo transcriptome assembly from RNA seq data: assembly of the duck (Anas platyrhynchos) transcriptome
... robust assembly to be produced by multiple methods without the need for very high memory ...of assembly obtained. For this dataset the use of MK in the assembly generated a more complete ...
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Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris
... of de novo assembled ...three assembly strategies for short-reads data, including the utility of haploid megagametophyte tissue during de novo assembly as single-allele guides, ...
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De novo transcriptome assembly and analysis of Sf21 cells using illumina paired end sequencing
... Pavan Kumar Kakumani 1 , Rohit Shukla 2 , Vivek N. Todur 2 , Pawan Malhotra 1* , Sunil K. Mukherjee 1,3* and Raj K. Bhatnagar 1* Abstract: Spodoptera is an important polyphagous agricultural insect pest in the tropical ...
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De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species
... initial assembly, strict filtering was used to remove duplicated, redundant, and low confidence ...available. Assembly completeness was assessed using three approaches, all of which supported high quality ...
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De-novo transcriptome assembly for gene identification, analysis, annotation, and molecular marker discovery in Onobrychis viciifolia
... The assembly, allowed us to identify 3786 ...a de novo assembly was easier to address than the development of SNPs, which is challenging with- out a reference ...combined assembly was ...
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Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads
... full-length transcriptome assembly by introducing the Branch- ing Measure, which is able to flag the transcripts that go through a complex region in the de Bruijn ...
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Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads
... full-length transcriptome assembly by introducing the Branch- ing Measure, which is able to flag the transcripts that go through a complex region in the de Bruijn ...
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De novo assembly and characterization of the transcriptome in the desiccation tolerant moss Syntrichia caninervis
... caninervis transcriptome using next-generation, RNA-Seq ...desiccation. De novo transcriptome assembly generated 92,240 unigene se- ...caninervis transcriptome and comparison ...
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Assembly and annotation of a non model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers
... sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species ...
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Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers
... sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species ...
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A quantitative reference transcriptome for Nematostella vectensis earlyembryonic development: a pipeline for de novo assembly in emergingmodel systems
... The de novo assembly of transcriptomes from short shotgun sequences raises challenges due to random and non-random sequencing biases and inherent transcript ...for de novo ...
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Deep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape
... and de novo transcriptome assembly at different stages of mouse ...our transcriptome assembly reveals that transcription correlates accurately with DNA methylation and accounts ...
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Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
... a de novo transcriptome assembly of Svevo, a modern elite durum wheat cultivar widely used in breeding ...several de novo assembly methods, we selected the CLC Workbench ...
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