Long reads: their purpose and place.
Martin O. Pollard,Deepti Gurdasani,Deepti Gurdasani,Alexander J. Mentzer,Tarryn Porter,Tarryn Porter,Manjinder S. Sandhu,Manjinder S. Sandhu +7 more
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TL;DR: This article will endeavour to present an introduction to long-read technologies showing: what long reads are; how they are distinct from short reads; whylong reads are useful and how they is being used.
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Abstract: In recent years long-read technologies have moved from being a niche and specialist field to a point of relative maturity likely to feature frequently in the genomic landscape. Analogous to next generation sequencing, the cost of sequencing using long-read technologies has materially dropped whilst the instrument throughput continues to increase. Together these changes present the prospect of sequencing large numbers of individuals with the aim of fully characterizing genomes at high resolution. In this article, we will endeavour to present an introduction to long-read technologies showing: what long reads are; how they are distinct from short reads; why long reads are useful and how they are being used. We will highlight the recent developments in this field, and the applications and potential of these technologies in medical research, and clinical diagnostics and therapeutics.
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Citations
Opportunities and challenges in long-read sequencing data analysis.
Shanika L. Amarasinghe,Shanika L. Amarasinghe,Shian Su,Shian Su,Xueyi Dong,Xueyi Dong,Luke Zappia,Matthew E. Ritchie,Matthew E. Ritchie,Quentin Gouil,Quentin Gouil +10 more
TL;DR: The current landscape of available tools is reviewed, the principles of error correction, base modification detection, and long-read transcriptomics analysis are focused on, and the challenges that remain are highlighted.
Long-read human genome sequencing and its applications.
TL;DR: The currently available platforms, how the technologies are being applied to assemble and phase human genomes, and their impact on improving the authors' understanding of human genetic variation are discussed.
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The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology.
Troy E. Sandberg,Michael J. Salazar,Liam L. Weng,Bernhard O. Palsson,Adam M. Feist,Adam M. Feist +5 more
TL;DR: This review summarizes and categorizes the applications of Adaptive Laboratory Evolution to various aspects of microbial physiology pertinent to industrial bioproduction by collecting case studies that highlight the multitude of ways in which evolution can facilitate the strain construction process.
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Long-Read Sequencing Emerging in Medical Genetics
TL;DR: The current LRS-based research on human genetic disorders is summarized and the potential of these technologies to facilitate the next major advancements in medical genetics is discussed.
Advances and Challenges in Metatranscriptomic Analysis.
TL;DR: A comprehensive review on computational metatranscriptomics approaches to study microbial community transcriptomes and a list of options for computational analysis of these data and will highlight areas in need of development.
References
Amplification-free, CRISPR-Cas9 Targeted Enrichment and SMRT Sequencing of Repeat-Expansion Disease Causative Genomic Regions
Yu-Chih Tsai,David Greenberg,James R. Powell,Ida Höijer,Adam Ameur,Maya Strahl,Ethan Ellis,Inger Jonasson,Ricardo Mouro Pinto,Vanessa C. Wheeler,Melissa Smith,Ulf Gyllensten,Robert Sebra,Jonas Korlach,Tyson A. Clark +14 more
TL;DR: A novel, amplification-free enrichment technique that employs the CRISPR-Cas9 system for specific targeting multiple genomic loci that enables enrichment and sequencing of complex genomic regions that cannot be investigated with other technologies.
Flexible and Scalable Full-Length CYP2D6 Long Amplicon PacBio Sequencing.
Henk P. J. Buermans,Rolf H. A. M. Vossen,Seyed Yahya Anvar,William G. Allard,Henk-Jan Guchelaar,Stefan J. White,Johan T. den Dunnen,Jesse J. Swen,Tahar van der Straaten +8 more
TL;DR: It is concluded that the CYP2D6 genotyping approach produces reliable CYP1D6 diplotypes and reveals information about additional variants, including phasing and copy‐number variation.
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