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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Sequencing and comparative analyses of the genomes of zoysiagrasses
Hidenori Tanaka,Hideki Hirakawa,Shunichi Kosugi,Shinobu Nakayama,Akiko Ono,Akiko Watanabe,Masatsugu Hashiguchi,Takahiro Gondo,Genki Ishigaki,Melody Muguerza,Katsuya Shimizu,Noriko Sawamura,Takayasu Inoue,Yuichi Shigeki,Naoki Ohno,Satoshi Tabata,Ryo Akashi,Shusei Sato +17 more
TL;DR: The information obtained in this study will be valuable for basic studies on zoysiagrass evolution and genetics as well as for the breeding of zoySIagrasses, and is made available in the ‘Zoysia Genome Database’.
Journal ArticleDOI
Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria
TL;DR: The results demonstrate that inherent sequence characteristics govern variation in coverage and suggest that some of this variation, like GC content, should be controlled for in, for example, RNA-Seq and detection of copy number variation.
Journal ArticleDOI
CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing
Yuchao Jiang,Rujin Wang,Eugene Urrutia,Ioannis N. Anastopoulos,Katherine L. Nathanson,Nan Zhang +5 more
TL;DR: CODEX2 is described, as a statistical framework for full-spectrum CNV profiling that is sensitive for variants with both common and rare population frequencies and that is applicable to study designs with and without negative control samples.
Journal ArticleDOI
Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice
Victor Greiff,Ulrike Menzel,Ulrike Haessler,Skylar C. Cook,Simon Friedensohn,Tarik A. Khan,Mark Pogson,Ina Hellmann,Sai T. Reddy +8 more
TL;DR: It is shown that both factors- replicate sequencing and sequencing depth-are crucial for robust CDR3 and VDJ detection and ranking and established widely applicable experimental and computational guidelines for robust antibody NGS and analysis, which will help advance systems immunology studies related to the quantitative profiling of antibody responses following infection and vaccination.
Y chromosome sequences reveal a short beringian standstill, rapid expansion, and early population structure of native american founders
Thomaz Pinotti,Thomaz Pinotti,Anders Bergström,Maria Geppert,Matt Bawn,Matt Bawn,Dominique Ohasi,Wentao Shi,Wentao Shi,Daniela R. Lacerda,Arne Solli,Jakob Norstedt,Kate Reed,Kim Dawtry,Fabricio González-Andrade,César Paz-y-Miño,Susana Revollo,Cinthia Cuellar,Marilza S. Jota,José Enemir dos Santos,Qasim Ayub,Qasim Ayub,Toomas Kivisild,Toomas Kivisild,José R. Sandoval,Ricardo Fujita,Yali Xue,Lutz Roewer,Fabrício R. Santos,Chris Tyler-Smith +29 more
TL;DR: A calibrated sequence-based analysis of 222 Native American and relevant Eurasian Y chromosomes from haplogroups Q and C identifies three to four independent lineages as autochthonous and likely founders: the major Q-M3 and rarer Q-CTS1780 present throughout the Americas, the very rare C3-MPB373 in South America, and possibly the C4-P39/Z30536 in North America.
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.