Journal ArticleDOI
Sequencing depth and coverage: key considerations in genomic analyses
TLDR
The issue of sequencing depth in the design of next-generation sequencing experiments is discussed and current guidelines and precedents on the issue of coverage are reviewed for four major study designs, including de novo genome sequencing, genome resequencing, transcriptome sequencing and genomic location analyses.Abstract:
Sequencing technologies have placed a wide range of genomic analyses within the capabilities of many laboratories. However, sequencing costs often set limits to the amount of sequences that can be generated and, consequently, the biological outcomes that can be achieved from an experimental design. In this Review, we discuss the issue of sequencing depth in the design of next-generation sequencing experiments. We review current guidelines and precedents on the issue of coverage, as well as their underlying considerations, for four major study designs, which include de novo genome sequencing, genome resequencing, transcriptome sequencing and genomic location analyses (for example, chromatin immunoprecipitation followed by sequencing (ChIP-seq) and chromosome conformation capture (3C)).read more
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Journal ArticleDOI
Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics
Jiangqin Zhao,Jikun Liu,Sai V. Vemula,Corinna Lin,Jiying Tan,Viswanath Ragupathy,Xue Wang,Christelle Mbondji-Wonje,Zhiping Ye,Marie L. Landry,Indira Hewlett +10 more
TL;DR: A “one-size-fits-all” approach using a next-generation sequencing (NGS) detection platform to extensively identify influenza viral genomes for diagnosis and determination of novel virulence and drug resistance markers is reported.
Journal ArticleDOI
Comparative transcriptome analysis of wild and lab populations of Astyanax mexicanus uncovers differential effects of environment and morphotype on gene expression.
Jaya Krishnan,Jenna L. Persons,Robert Peuß,Huzaifa Hassan,Alexander Kenzior,Shaolei Xiong,Luke A. Olsen,Luke A. Olsen,Ernesto Maldonado,Johanna E. Kowalko,Nicolas Rohner,Nicolas Rohner +11 more
TL;DR: It is concluded that a controlled laboratory environment may serve as an ideal setting to study the genetic underpinnings of metabolic and physiological differences between the cavefish and surface fish.
Journal ArticleDOI
Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.
Cindy Verdu,Erwan Guichoux,Samuel Quevauvillers,Olivier De Thier,Yec’han Laizet,Adline Delcamp,Frédéric Gévaudant,Arnaud Monty,Annabel J. Porté,Philippe Lejeune,Ludivine Lassois,Stéphanie Mariette +11 more
TL;DR: Using the strategy developed here, more than 80% of the SNPs tested by means of individual genotyping were able to validate, resulting in a readily usable set of 330 SNPs, suitable for use in population genetics applications.
Journal ArticleDOI
GROM-RD: resolving genomic biases to improve read depth detection of copy number variants
TL;DR: GROM-RD, an algorithm that analyzes multiple biases in read coverage to detect CNVs in NGS data and employs a CNV search using size-varying overlapping windows to improve breakpoint resolution, is developed and compared to two widely used programs based on read depth methods, CNVnator and RDXplorer, and observed improved CNV detection and breakpoint accuracy.
Journal ArticleDOI
Whole genome sequences in pulse crops: a global community resource to expedite translational genomics and knowledge-based crop improvement
Abhishek Bohra,Narendra Singh +1 more
TL;DR: It is anticipated that the crop improvement schemes will be bolstered remarkably with rational deployment of these genome-guided approaches, ultimately resulting in expanded plant breeding capacities and improved crop performance.
References
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Journal ArticleDOI
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TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Journal ArticleDOI
Differential expression analysis for sequence count data.
Simon Anders,Wolfgang Huber +1 more
TL;DR: A method based on the negative binomial distribution, with variance and mean linked by local regression, is proposed and an implementation, DESeq, as an R/Bioconductor package is presented.
Journal ArticleDOI
RNA-Seq: a revolutionary tool for transcriptomics
TL;DR: The RNA-Seq approach to transcriptome profiling that uses deep-sequencing technologies provides a far more precise measurement of levels of transcripts and their isoforms than other methods.
Journal ArticleDOI
TopHat: discovering splice junctions with RNA-Seq
TL;DR: The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer.