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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Beyond fruit-flies: population genomic advances in non-Drosophila arthropods
TL;DR: The progress of genome projects in non-Drosophila arthropods is reviewed, focusing on advances in the analysis of large-scale polymorphism data and functional genomics and examples of population genomic studies.
Journal ArticleDOI
Sanger Validation of High-Throughput Sequencing in Genetic Diagnosis: Still the Best Practice?
Rosina De Cario,Ada Kura,Samuele Suraci,Alberto Magi,Andrea Volta,Rossella Marcucci,Anna Maria Gori,Guglielmina Pepe,Betti Giusti,Elena Sticchi +9 more
TL;DR: This study extends literature data in which almost 100% “high quality” NGS variants are confirmed by Sanger, and demonstrates that in case of discrepancy between a high-quality NGS variant and Sanger validation, NGS call should not be a priori assumed to represent the source of the error.
Journal ArticleDOI
Differentiation of G:C vs A:T and G:C vs G:mC Base Pairs in the Latch Zone of α-Hemolysin
TL;DR: A series of duplexes were probed in the latch zone to establish if this region can detect more subtle features of base pairs beyond the complete absence of a base and demonstrate that the most sensitive region of the latch can readily discriminate duplexe in which one G:C base pair is replaced by an A:T.
Journal ArticleDOI
Genetic Variants Contributing to Early Recurrent Pregnancy Loss Etiology Identified by Sequencing Approaches.
TL;DR: The information given here should be useful for clinicians, scientists, and students to enable a better understanding of RPL etiology and provide a basis for the development of diagnostic/prognostic approaches contributing toward translational medicine.
Journal ArticleDOI
Marine health of the Arabian Gulf: Drivers of pollution and assessment approaches focusing on desalination activities
Hoda Ali Hosseini,Imen Saadaoui,Navid R. Moheimani,Mohammad Al Saidi,Fahad Al Jamali,Hareb Al Jabri,Radhouane Ben Hamadou +6 more
TL;DR: In this article, the potential negative effects of desalination plants on the Arabian Gulf's marine environments were revealed. But, the authors emphasized the significance of national regulations and regional cooperation to tackle the issue.
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.