Next-Generation Sequencing Data Analysis (Hardcover)

Xinkun Wang

  • 出版商: CRC
  • 出版日期: 2016-02-24
  • 售價: $4,370
  • 貴賓價: 9.5$4,152
  • 語言: 英文
  • 頁數: 258
  • 裝訂: Hardcover
  • ISBN: 1482217880
  • ISBN-13: 9781482217889
  • 相關分類: Data Science
  • 已絕版

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商品描述

A Practical Guide to the Highly Dynamic Area of Massively Parallel Sequencing

 

The development of genome and transcriptome sequencing technologies has led to a paradigm shift in life science research and disease diagnosis and prevention. Scientists are now able to see how human diseases and phenotypic changes are connected to DNA mutation, polymorphism, genome structure, and epigenomic abnormality. Next-Generation Sequencing Data Analysis shows how next-generation sequencing (NGS) technologies are applied to transform nearly all aspects of biological research.

 

The book walks readers through the multiple stages of NGS data generation and analysis in an easy-to-follow fashion. It covers every step in each stage, from the planning stage of experimental design, sample processing, sequencing strategy formulation, the early stage of base calling, reads quality check and data preprocessing to the intermediate stage of mapping reads to a reference genome and normalization to more advanced stages specific to each application. All major applications of NGS are covered, including:

  • RNA-seq: mRNA-seq and small RNA-seq
  • Genotyping and variant discovery through genome re-sequencing
  • De novo genome assembly
  • ChIP-seq to study DNA–protein interaction
  • Methylated DNA sequencing on epigenetic regulation
  • Metagenome analysis through community genome shotgun sequencing

 

Before detailing the analytic steps for each of these applications, the book presents the ins and outs of the most widely used NGS platforms, with side-by-side comparisons of key technical aspects. This helps practitioners decide which platform to use for a particular project. The book also offers a perspective on the development of DNA sequencing technologies, from Sanger to future-generation sequencing technologies.

 

The book discusses concepts and principles that underlie each analytic step, along with software tools for implementation. It highlights key features of the tools while omitting tedious details to provide an easy-to-follow guide for practitioners in life sciences, bioinformatics, and biostatistics. In addition, references to detailed descriptions of the tools are given for further reading if needed. The accompanying website for the book provides step-by-step, real-world examples of how to apply the tools covered in the text to research projects. All the tools are freely available to academic users.

商品描述(中文翻譯)

《大規模並行序列分析的實用指南》

基因組和轉錄組测序技術的發展引起了生命科學研究和疾病診斷與預防的範式轉變。科學家現在能夠看到人類疾病和表型變化與DNA突變、多態性、基因組結構和表觀遺傳異常之間的聯繫。《下一代测序數據分析》展示了如何應用下一代测序(NGS)技術來轉變生物學研究的幾乎所有方面。

本書以易於理解的方式引導讀者進行NGS數據生成和分析的多個階段。它涵蓋了每個階段的每個步驟,從實驗設計的計劃階段、樣本處理、测序策略制定、基礎呼叫的早期階段、讀數質量檢查和數據預處理,到將讀數映射到參考基因組和正規化等中級階段,再到每個應用特定的更高級階段。涵蓋了NGS的所有主要應用,包括:

- RNA-seq:mRNA-seq和small RNA-seq
- 通過基因組重测序進行基因型和變異發現
- 从头組装基因組
- ChIP-seq研究DNA-蛋白質相互作用
- 甲基化DNA测序研究表觀遺傳調控
- 通過社區基因組shotgun测序進行宏基因組分析

在詳細介紹這些應用的分析步驟之前,本書介紹了最常用的NGS平台的細節,並進行了關鍵技術方面的比較。這有助於從業人員決定在特定項目中使用哪個平台。本書還提供了關於DNA测序技術發展的觀點,從Sanger到未來的下一代测序技術。

本書討論了每個分析步驟的概念和原則,以及實施的軟件工具。它突出了工具的關鍵特點,同時省略了繁瑣的細節,為生命科學、生物信息學和生物統計學從業人員提供了易於遵循的指南。此外,如果需要,還提供了有關工具的詳細描述的參考資料。本書的附帶網站提供了如何將文本中涵蓋的工具應用於研究項目的逐步實例。所有這些工具都可以免費提供給學術用戶使用。