de novo assembly
A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes
... genome assembly to be used as a reference genome by applying bioinformatic ...guided de novo assembly approach could be useful in facilitating the generation of other mitochondrion sequences, ...
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De novo assembly of a genome-wide transcriptome map of Vicia faba (L.) for transfer cell research
... undertaken de novo assembly of a genome-wide transcriptome map for ...for assembly following trimming and quality control. Assembly using a De-Bruijn graph-based approach ...
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De novo assembly of bacterial transcriptomes from RNA seq data
... for de novo assembly of bac- terial transcriptomes, which we have implemented in the system Rockhopper ...for de novo assembly of bacterial transcriptomes outperform other ...
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De novo assembly and annotation of Hyalomma dromedarii tick (Acari: Ixodidae) sialotranscriptome with regard to gender differences in gene expression
... Background: Hard ticks are hematophagous ectoparasites characterized by their long-term feeding. The saliva that they secrete during their blood meal is their crucial weapon against host-defense systems including ...
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ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly
... We tested our algorithm and the existing indel detection methods for sensitivity and specificity of clinically rele- vant indels in cancer with custom-designed amplicon NGS data. We first trimmed the 5’ adapter sequence ...
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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 transcriptome ...
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De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome
... the assembly of a comprehensive and high quality transcriptome from nine different tissue types, and eight larval and post-larval early life-history stages of the black tiger shrimp, Penaeus ...high-quality ...
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De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads
... Using the FASTQ files, rather than just reads from the called pass bin, allowed a maximum amount of sequence information to be recovered. Reads were trimmed by 65 bp at each end to exclude adapters (see below), then Canu ...
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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
... Acquisition of DNAme at a genomic locus is likely to require integration of a combination of several factors, such as DNA sequence, specific trans-acting factors, and cross-talk between histone modifications and DNA ...
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Characterization of the Ren4 resistance locus through the integration of de novo assembly, expression analysis, and Genotyping-by-Sequencing data
... BAC assembly was generated using Velvet and SSPACE. This assembly spanned ...Two de novo transcriptomes were generated using Trinity for the wild source of Ren4 and a Ren4 introgression ...
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De novo assembly of potential linear artificial chromosome constructs capped with expansive telomeric repeats
... either de novo artificial chromo- somes or engineered minichromosomes can be grouped into two broad categories: the “top-down” and “bottom- up” approaches, ...
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The Utility of Data Transformation for Alignment, de novo Assembly and Classification of Short Read Virus Sequences
... of short reads, used time series and digital signal processing data transformation techniques.. Figure 190.[r] ...
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Transcriptome Analysis of the Ark Shell Scapharca subcrenata: De Novo Assembly, Identification of Genes and Pathways Involved in Growth
... 2.3 Analysis of differentially expressed genes in fast- and slow-growing groups 123.. The count of the expressed tags was separately calculated for each library and used to 124.[r] ...
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Poly(rC) Binding Proteins and the 5′ Cloverleaf of Uncapped Poliovirus mRNA Function during De Novo Assembly of Polysomes
... Poliovirus (PV) mRNA is unusual because it possesses a 5 ⴕ -terminal monophosphate rather than a 5 ⴕ - terminal cap. Uncapped mRNAs are typically degraded by the 5 ⴕ exonuclease XRN1. A 5 ⴕ -terminal cloverleaf RNA ...
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Pattern formation during de novo assembly of the Arabidopsis shoot meristem
... (Haberlandt, 1902). Our study represents an early step towards realizing this potential. In vitro culture experiments support the idea that cell identity in plants is largely governed by positional cues mediated by ...
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Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria
... Metagenome assembly, binning, and annotation. 454 pyrosequenc- ing reads were assembled using the Newbler assembler (Roche) with de- fault parameter settings except that the “large” flag was used. Contigs ...
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Performance characterization of de novo genome assembly on leading parallel systems
... In this section we describe the basic algorithms used in the pipeline, our par- allelization strategy, and the consequent communication patterns. Although we focus on HipMer, the algorithms are relevant to all de ...
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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 that contains high quality ...MK assembly), however we believe the 6 SK assembly represents a more cautious assembly by reducing potential false positive tran- ...SK ...
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Accuracy assessment of fusion transcript detection via read mapping and de novo fusion transcript assembly based methods
... transcript assembly: JAFFA-Assembly [32] and three execution modes of Tri- nityFusion: TrinityFusion-C, TrinityFusion-D, and ...and de novo assembly ...involving assembly of all ...
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Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus)
... and assembly, where it is now possible for individual re- searchers to produce genome assemblies for organisms of their ...high-quality de novo eukaryotic genome assemblies. An ideal de ...
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