de novo genome assembly
Assisted assembly: how to improve a de novo genome assembly by using related species
... Assisted assembly principle Figure 1 (see previous page) Assisted assembly ...reference genome, and the two leftmost of these (purple) also appear as the two rightmost reads in an existing de ...
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Assisted assembly: how to improve a de novo genome assembly by using related species
... http://genomebiology.com/2009/10/8/R88 Genome Biology 2009, Volume 10, Issue 8, Article R88 Gnerre et ...de novo assembly, single read pair links cannot be used to join scaffolds, because even with a ...
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Assisted assembly: how to improve a de novo genome assembly by using related species
... Assisted assembly principle Figure 1 (see previous page) Assisted assembly ...reference genome, and the two leftmost of these (purple) also appear as the two rightmost reads in an existing de ...
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Improving transcriptome de novo assembly by using a reference genome of a related species: Translational genomics from oil palm to coconut
... given genome [ 12 ...reference genome, de novo transcriptomes undergo several drawbacks [ 13 ...de novo assembly, has a high resilience to chimerism, while this software and some others ...
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High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome.
... arboricolus genome sequence to ...paradoxus assembly [15], which was based on Sanger sequence reads (that do not suffer from homopolymer errors), shows less than half the number of frame-shifts than ...de ...
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Illumina and PacBio DNA sequencing data, de novo assembly and annotation of the genome of Aurantiochytrium limacinum strain CCAP_4062/1
... de novo assembly, and annotation of the complete genome of a new thraustochytrid species, strain ...Draft genome sequence of the docosahex- aenoic acid producing thraustochytrid ...
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FAssem : FPGA based Acceleration of De Novo Genome Assembly
... large genome containing millions of base-pairs (the size ¿ of the human genome = 3x109 ...Sequence Assembly is a computational biology problem where the genome is assembled using the reads ...
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RH mapping by sequencing: chromosome-scale assembly of the duck genome
... whole genome project of a high eukaryote, namely the human genome closely following the fruit fly genome, thousands of genomes have been sequenced [1] thanks to the emergence of massively parallel ...
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A High Quality Draft Assembly of the Diploid 'Regina' Sweet Cherry Genome
... de novo assembled using FALCON assembler and phased using FALCON ...whole genome maps were used for further scaffolding. Our de novo genome assembly resulted in a genome of 279 ...
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Computational methods for de novo assembly of next-generation genome sequencing data
... 4.5 Discussion In this chapter, we introduced two novel ingredients for efficiently assembling paired reads. First, we studied how to perform traversal of paired string graphs in the ideal case. The notion of ...
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Ten steps to get started in Genome Assembly and Annotation
... ware, assembly with or without pre-processing of the sequence data, and also with different parameter ...the assembly is the use of mate pair ...the assembly technology, but also in increasing read ...
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<em>De novo</em> genome and transcriptome resources of the Adzuki bean borer <em>Ostrinia scapulalis</em> (Lepidoptera: Crambidae)
... corresponding to these various stages and tissues ( Table 5 ). RNA quality and concentration were evaluated using the RNA 6000 Nano kit with an Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA). ...
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Chromosome‐level hybrid de novo genome assemblies as an attainable option for non‐model insects
... de novo genome ...on genome evolution for a number of non-model ...de novo, chromosome-level genome ...hybrid genome assembly, sequence correction and manipulation are ...
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Daclatasvir Prevents Hepatitis C Virus Infectivity by Blocking Transfer of Viral Genome to Assembly Sites.
... both assembly and DMV biogenesis events resistant to DCV, 6,9 it implies that DCV targets a mutual, specific NS5A function that inhibits both ...de novo expressed non- structural proteins would tend to ...
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Whole-genome assembly of Akkermansia muciniphila sequenced directly from human stool
... of genome sequencing for Akkermansia muciniphila directly from the stool sample collected from one of these ...and assembly using metagenomic data obtained from the stool ...reference genome of the ...
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The Chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data
... Discussion cpn60 (also known by synonyms GroEL and Hsp60) is a molecular chaperone conserved in Bacteria and in Eukaryotes [37]. The cpn60 UT sequence, accessible by PCR using degenerate broad-range (‘‘universal’’) ...
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De novo assembly and annotation of the retinal transcriptome for the Nile grass rat (Arvicanthis ansorgei)
... and degeneration and for the identification of cone specific genes, pathways, and mechanisms that promote homeostasis and survival. A significant hurdle for molecular studies in A. ansorgei, however, is that there is ...
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Draft genome assembly and annotation of the gila topminnow Poeciliopsis occidentalis
... de novo gene ...de novo using RepeatModeler ( Smit et ...the genome assembly, and their location was collected as intergenic ...the genome assembly with ...
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Assemblage de novo avec Spark
... [2] E. Bourreau, A. Chateau, C. Dallard, and R. Giroudeau. Une modèlisation par contraintes de graphe pour résoudre l’échafaudage de génome. In ROADEF, 2017. [3] Genome Assembly Gold-Standard Evaluations. ...
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Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential
... optical genome map (Supplementary Tables ...estimated genome size) was arranged first into super-scaffolds (N50 > 29 megabases, Mb) and then into ...the assembly to confirm a near-unimodal ...
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