Long walk to genomics: History and current approaches to genome sequencing and assembly

机译：基因组学的漫漫长路：基因组测序和组装的历史和当前方法

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摘要

Genomes represent the starting point of genetic studies. Since the discovery of DNA structure, scientists have devoted great efforts to determine their sequence in an exact way. In this review we provide a comprehensive historical background of the improvements in DNA sequencing technologies that have accompanied the major milestones in genome sequencing and assembly, ranging from early sequencing methods to Next-Generation Sequencing platforms. We then focus on the advantages and challenges of the current technologies and approaches, collectively known as Third Generation Sequencing. As these technical advancements have been accompanied by progress in analytical methods, we also review the bioinformatic tools currently employed in genome assembly, as well as some applications of Third Generation Sequencing technologies and high-quality reference genomes.

机译：基因组代表了遗传研究的起点。自从发现DNA结构以来，科学家们一直在努力以精确的方式确定其序列。在这篇综述中，我们提供了DNA测序技术改进的全面历史背景，这些技术伴随着基因组测序和组装的主要里程碑，从早期测序方法到下一代测序平台。然后，我们集中讨论当前技术和方法（统称为第三代测序）的优势和挑战。由于这些技术进步伴随着分析方法的进步，我们还将回顾当前在基因组装配中使用的生物信息学工具，以及第三代测序技术和高质量参考基因组的一些应用。

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期刊名称 Computational and Structural Biotechnology Journal
作者
Alice Maria Giani; Guido Roberto Gallo; Luca Gianfranceschi; Giulio Formenti;
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作者单位

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年(卷),期 2020(18),-1
年度 2020
页码 -1
总页数 11
原文格式 PDF
正文语种
中图分类生物学;
关键词
BAC; Bacterial Artificial Chromosome; bp; base pair; ddNTP; 23-dideoxynucleoside triphosphate; dNTPs; deoxynucleoside triphosphates; HapMap; haplotype map; HGP; Human Genome Project; HMW; high molecular weight; NGS; Next Generation Sequencing; OLC; Overlap-Layout-Consensus; QV; Quality Value (QV); SBS; Sequencing by Synthesis; SMRT; Single Molecule Real-Time; SNPs; Single Nucleotide Polymorphisms; SRA; Short Read Archive; SV; Structural Variant; TGS; Third Generation Sequencing; WGS; Whole Genome Sequencing; ZMW; Zero-Mode Waveguide;

机译：BAC;细菌人工染色体;bp;碱基对;ddNTP;23-二脱氧核苷三磷酸;dNTPs;三磷酸脱氧核苷;HapMap;单倍型图;HGP;人类基因组计划;分子量;高分子量;NGS;下一代测序;OLC;重叠布局共识;QV;质量值（QV）;SBS;合成测序;SMRT;单分子实时;单核苷酸多态性SRA;短读存档;SV;结构变体;TGS;第三代测序;WGS;全基因组测序;ZMW;零模波导;

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专利

1. Long walk to genomics: History and current approaches to genome sequencing and assembly [J] . Alice Maria Giani, Guido Roberto Gallo, Luca Gianfranceschi, Computational and Structural Biotechnology Journal . 2020,第1期

机译：漫步到基因组学：历史和目前基因组测序和组装的方法
2. De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome [J] . Massimo Iorizzo, Douglas Senalik, Marek Szklarczyk, BMC Plant Biology . 2012,第1期

机译：使用下一代全基因组DNA测序从头组装胡萝卜线粒体基因组，为DNA转移到被子植物质体基因组中提供了第一个证据
3. Next-Generation Sequencing and De Novo Assembly, Genome Organization, and Comparative Genomic Analyses of the Genomes of Two Helicobacter pylori Isolates from Duodenal Ulcer Patients in India [J] . Narender Kumar, Asish K. Mukhopadhyay, Rajashree Patra, Journal of bacteriology . 2012,第21期

机译：来自印度十二指肠溃疡患者的两种幽门螺杆菌分离株的下一代测序和从头组装，基因组组织和比较基因组分析
4. APPLICATION OF GENOME LINGUISTIC APPROACHES FOR IDENTIFICATION OF GENOMIC ISLAND IN BACTERIAL GENOMES AND TRACKING DOWN THEIR ORIGINS: Genome Linguistics to Visualize Horizontal Gene Exchange [C] . Oliver Bezuidt, Kingdom Mncube, Oleg N. Reva International Conference on Bioinformatics Models, Methods and Algorithms . 2012

机译：基因组语言方法在细菌基因组中鉴定基因组语言探测及跟踪它们的起源：基因组语言学可视化水平基因交换
5. Improving eukaryotic genome assembly through application of single molecule real-time sequencing data genome: Coffee Leaf Rust fungus, H. vastatrix [D] . Adetunji, Modupeore O. 2014

机译：通过应用单分子实时测序数据基因组改善真核基因组组装：咖啡叶防锈真菌，H.pastatrix
6. Next-Generation Sequencing and De Novo Assembly Genome Organization and Comparative Genomic Analyses of the Genomes of Two Helicobacter pylori Isolates from Duodenal Ulcer Patients in India [O] . Narender Kumar, Asish K. Mukhopadhyay, Rajashree Patra, 2012

机译：印度十二指肠溃疡患者的两种幽门螺杆菌分离株的下一代测序和从头测序基因组组织和比较基因组分析
7. De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome [O] . Massimo Iorizzo, Douglas Senalik, Marek Szklarczyk, 2012

机译：从头开始使用下一代全基因组DNA测序技术对胡萝卜线粒体基因组进行重新组装，为DNA转移到被子植物质体基因组中提供了首个证据

Long walk to genomics: History and current approaches to genome sequencing and assembly

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