Browsing by Subject "High-throughput sequencing"

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    Evaluation of genome scaffolding tools using pooled clone sequencin
    (Scientific and Technical Research Council of Turkey, 2018) Dal, Elif; Alkan, Can
    DNA sequencing technologies hold great promise in generating information that will guide scientists to understand how the genome affects human health and organismal evolution. The process of generating raw genome sequence data becomes cheaper and faster, but more error-prone. Assembly of such data into high-quality finished genome sequences remains challenging. Many genome assembly tools are available, but they differ in terms of their performance and their final output. More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. Here we evaluate the accuracies of several genome scaffolding algorithms using two different types of data generated from the genome of the same human individual: whole genome shotgun sequencing (WGS) and pooled clone sequencing (PCS). We observe that it is possible to obtain better assemblies if PCS data are used, compared to using only WGS data. However, the current scaffolding algorithms are developed only for WGS, and PCS-aware scaffolding algorithms remain an open problem.
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    ItemOpen Access
    Inter-varietal structural variation in grapevine genomes
    (Wiley-Blackwell Publishing Ltd., 2016) Cardone, M. F.; D'Addabbo, P.; Alkan C.; Bergamini, C.; Catacchio, C. R.; Anaclerio, F.; Chiatante, G.; Marra, A.; Giannuzzi, G.; Perniola, R.; Ventura M.; Antonacci, D.
    Grapevine (Vitis vinifera L.) is one of the world's most important crop plants, which is of large economic value for fruit and wine production. There is much interest in identifying genomic variations and their functional effects on inter-varietal, phenotypic differences. Using an approach developed for the analysis of human and mammalian genomes, which combines high-throughput sequencing, array comparative genomic hybridization, fluorescent in�situ hybridization and quantitative PCR, we created an inter-varietal atlas of structural variations and single nucleotide variants (SNVs) for the grapevine genome analyzing four economically and genetically relevant table grapevine varieties. We found 4.8 million SNVs and detected 8% of the grapevine genome to be affected by genomic variations. We identified more than 700 copy number variation (CNV) regions and more than 2000 genes subjected to CNV as potential candidates for phenotypic differences between varieties