Next Generation Sequencing Assembly
Computational methods for de novo assembly of next-generation genome sequencing data
... Parallel indexing speed-up Then, we computed the full indexing time for an increasing number of cores (Figure 4- 9 ). Note that a significant overhead occurs, which ultimately limits the benefits of parallel processing. ...
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NG6: Integrated next generation sequencing storage and processing environment.
... 454 sequencing kits include control fragments known as spike-ins within each ...the next step reads are cleaned using the pyrocleaner script ...novo assembly is performed on the cleaned reads using ...
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Next generation sequencing elucidates cacao badnavirus diversity and reveals the existence of more than ten viral species
... DNA sequencing and de novo assembly Extracted DNA underwent rolling circle amplification (RCA, TempliPhi kit, GE Healthcare Life Science) to concentrate/enrich the sample with circular forms and was sent to ...
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Targeted next generation sequencing with an extended gene panel does not impact variant detection in mitochondrial diseases
... exactly the same clinical signs with same onset but she was not available for testing. At the age of 69, muscle bi- opsy revealed COX-negative fibers with a complex IV deficiency by spectrophotometry. Blue native PAGE ...
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Unraveling the sperm transcriptome by next generation sequencing and the global epigenetic landscape in infertile men
... 39 EIF4G2, ILF2. To note, the ribosomal proteins are involved in the assembly of the ribosomes in the mitochondria and a disrupted function of the mitochondria can cause asthenozoospermia. Additionally, some ...
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Hybrid Capture-Based Next Generation Sequencing and Its Application to Human Infectious Diseases
... genome assembly and detection of single nucleotide variants of Lassa virus (LASV) from ultra-low input samples ( Matranga et ...shotgun sequencing could also be performed using a combination of several ...
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Next-generation sequencing of 16S ribosomal RNA gene amplicons
... The primers used here amplified the variable regions 3 and 4 from the 16S rRNA gene, but many other regions could be targeted. In present study, 16S rRNA genes were amplified from plant material and the choice of primer ...
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Next-generation sequencing confirms the implication of SLC24A1 in autosomal-recessive congenital stationary night blindness
... 37. Bujakowska KM, Zhang Q, Siemiatkowska AM et al. Mutations in IFT172 cause isolated retinal degeneration and Bardet-Biedl syndrome. Hum Mol Genet 2015: 24: 230-242. 38. Boulanger-Scemama E, El Shamieh S, Demontant V ...
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Identification of novel APOB mutations by targeted next-generation sequencing for the molecular diagnosis of familial hypobetalipoproteinemia
... [16] M.J. Chapman, S. Goldstein, D. Lagrange, P.M. Laplaud, A density gradient ultracentrifugal procedure for the isolation of the major lipoprotein classes from human serum, J. Lipid Res. 22 (1981) 339e358 . [17] A.B. ...
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Exploring optimal snoRNA profiling using Next Generation Sequencing methods
... as sequencing technologies are concerned is the reverse transcriptase (Mohr et ...creating sequencing libraries, the RT can be isolated from the rest of the group II intron complex (Enyeart et ...illumina ...
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Advanced Characterization of DNA Molecules in rAAV Vector Preparations by Single-stranded Virus Next-generation Sequencing
... An in silico control was generated to mimic a real NGS library and to determine the prediction accuracy of the map- ping software using Fastq Control Sampler, a custom C program. The open source code for the software is ...
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Application of next generation sequencing for study and diagnosis of plant viral diseases in agriculture
... Viral threat: Plant viruses cause millions of Euros of damages in food security, quality and grower income.. Sensitive and reliable diagnostics are key for their control[r] ...
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Next-generation sequencing for rodent barcoding: species identification from fresh, degraded and environmental samples
... common sequencing errors were insertions, likely due to homopolymer stretches, and which were detected in more than 20% of the reads generated for our internal ...
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Molecular diagnosis of inherited peripheral neuropathies by targeted next-generation sequencing: molecular spectrum delineation
... constantly rising, and is now above 100. Our objective is to compare the diagnostic yield of a targeted NGS strategy (panel of 81 IPN/CMT genes) with the previous gene by gene Sanger sequencing strategy, by ...
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Analysis of Somatic Alterations in Cancer Genome: From SNP Arrays to Next Generation Sequencing
... targeted sequencing (for ex- ample, whole exome sequencing), in addition to mappability and GC-content, a bias resulting from uneven capture in different targeted regions should also be corrected (Li et ...
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Detection and identification of transgenic events by next generation sequencing combined with enrichment technologies.
... The analysed samples included five species, eight transgenic events and variable fractions (0.1%, 1%, 10% and 100%) of GMOs (Table 2 in the methods section). Concerning GMO detection, the structural elements listed in ...
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Isolation of TGF-β-neutralizing single-domain antibodies of predetermined epitope specificity using next-generation DNA sequencing
... plates were coated overnight at 4°C with 0.1 μg TGF-β3 in 35 μL PBS. The next day, wells were blocked with 200 μL of PBS containing 2% BSA for 1 h at 37°C, then sdAbs were diluted in PBS containing 1% BSA and 0.1% ...
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Next-generation SDN based virtualized networks
... In this thesis, I presented the work done during my three years of PhD which tackled the scalability, performance and energy efficiency problems to build next-generation SDN based vir- tualized networks. We ...
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Next Generation Internet Research and Experimentation
... Future Internet systems will integrate a broad range of systems (cloud services, sensor networks, content platforms, etc.) in large-scale hetero- geneous systems-of-systems. There is a growing need for integration e.g. ...
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Le next-generation biobanking - Un défi des données numériques
... SUMMARY Next generation biobanking: the challenge of data Human biological samples are key resources in unrav- elling physiopathological factors underlying diseases and influencing their ...
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