Sequence assembly using next generation sequencing data—challenges and solutions
نویسندگان
چکیده
منابع مشابه
Strategies and Clinical Applications of Next Generation Sequencing
Abstract DNA sequencing is one of the great valuable techniques in molecular biology, which can be used to detect the sequence of nucleotides in a DNA fragment. The high-throughput sequencing known as Next Generation Sequencing (NGS) revolutionized genomic research and molecular biology; therefore, the whole human genome can be sequenced with a low cost in several days. NGS technology is simi...
متن کاملStrategies and Clinical Applications of Next Generation Sequencing
Abstract DNA sequencing is one of the great valuable techniques in molecular biology, which can be used to detect the sequence of nucleotides in a DNA fragment. The high-throughput sequencing known as Next Generation Sequencing (NGS) revolutionized genomic research and molecular biology; therefore, the whole human genome can be sequenced with a low cost in several days. NGS technology is simi...
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High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads to properly reconstruct repetitive sequences. The mathematical model shows the upper limits of accuracy of the results as a function of read coverage. For hig...
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Due to the complexity of the protocols and a limited knowledge of the nature of microbial communities, simulating metagenomic sequences plays an important role in testing the performance of existing tools and data analysis methods with metagenomic data. We developed metagenomic read simulators with platform-specific (Sanger, pyrosequencing, Illumina) base-error models, and simulated metagenomes...
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The emergence of next-generation sequencing platforms led to resurgence of research in whole-genome shotgun assembly algorithms and software. DNA sequencing data from the Roche 454, Illumina/Solexa, and ABI SOLiD platforms typically present shorter read lengths, higher coverage, and different error profiles compared with Sanger sequencing data. Since 2005, several assembly software packages hav...
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ژورنال
عنوان ژورنال: Science China Life Sciences
سال: 2014
ISSN: 1674-7305,1869-1889
DOI: 10.1007/s11427-014-4752-9