Repetitive dna and next-generation sequencing computational challenges and solutions pdf

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repetitive dna and next-generation sequencing computational challenges and solutions pdf

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DNA sequencing is the process of determining the nucleic acid sequence — the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine , guanine , cytosine , and thymine.

Repetitive DNA and next-generation sequencing: computational challenges and solutions

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Next-generation sequencing NGS technologies have fostered an unprecedented proliferation of high-throughput sequencing projects and a concomitant development of novel algorithms for the assembly of short reads. However, numerous technical or computational challenges in de novo assembly still remain, although many new ideas and solutions have been suggested to tackle the challenges in both experimental and computational settings. In this review, we first briefly introduce some of the major challenges faced by NGS sequence assembly. Then, we analyze the characteristics of various sequencing platforms and their impact on assembly results. After that, we classify de novo assemblers according to their frameworks overlap graph-based, de Bruijn graph-based and string graph-based , and introduce the characteristics of each assembly tool and their adaptation scene. Next, we introduce in detail the solutions to the main challenges of de novo assembly of next generation sequencing data, single-cell sequencing data and single molecule sequencing data. This review not only gives an overview of the latest methods and developments in assembly algorithms, but also provides guidelines to determine the optimal assembly algorithm for a given input sequencing data type.

Next Generation Sequencing in Aquatic Models

The most valuable application of next generation sequencing NGS technology is genome sequencing. Genomes of several aquatic models had been sequenced in the past few years due to their importance in genomics, development biology, toxicology, pathology, and cancer research. NGS technology is greatly advanced in sequencing length and accuracy, which facilitate the sequencing process, but sequence assembly, especially for the species with complicated genomes, is still the biggest challenge for bench-top scientists. Next generation sequencing NGS technology has been broadly used in biomedical research. The most valuable application of this technology is genome and transcriptome sequencing, which form a bridge to link fundamental discoveries in research using disease model systems to clinical application. Aquatic animal models are widely used in genomics, development biology, toxicology, pathology, and cancer research for a recent review, see [ 1 ]. The genomes of several aquatic models had been sequenced using NGS technology over the past few years [ 2 , 3 ].

Skip to search form Skip to main content You are currently offline. Some features of the site may not work correctly. DOI: Treangen and S. Treangen , S. Repetitive DNA sequences are abundant in a broad range of species, from bacteria to mammals, and they cover nearly half of the human genome. Repeats have always presented technical challenges for sequence alignment and assembly programs.

DNA sequencing

Background: Next-generation sequencing NGS technologies have fostered an unprecedented proliferation of high-throughput sequencing projects and a concomitant development of novel algorithms for the assembly of short reads. However, numerous technical or computational challenges in de novo assembly still remain, although many new ideas and solutions have been suggested to tackle the challenges in both experimental and computational settings. Results: In this review, we first briefly introduce some of the major challenges faced by NGS sequence assembly. Then, we analyze the characteristics of various sequencing platforms and their impact on assembly results. After that, we classify de novo assemblers according to their frameworks overlap graph-based, de Bruijn graph-based and string graph-based , and introduce the characteristics of each assembly tool and their adaptation scene.

Erratum: Repetitive DNA and next-generation sequencing: computational challenges and solutions

Metrics details. Repetitive DNA motifs — not coding genetic information and repeated millions to hundreds of times — make up the majority of many genomes. Fluorescence in situ hybridization FISH -based karyotypes are developed to understand chromosome and repetitive sequence evolution of common oat.

Skip to search form Skip to main content You are currently offline. Some features of the site may not work correctly. DOI: Treangen and S.

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