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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HRT Atlas v1.1 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets
TL;DR: This work presents Housekeeping Transcript Atlas (HT Atlas v1.0, www.housekeeping.unicamp.br) a web-based database which addresses some of the previously observed limitations in the identification of these genes, and offers a more accurate database of human and mouse HK genes and transcripts.
Journal ArticleDOI
Comparison of sequencing methods and data processing pipelines for whole genome sequencing and minority single nucleotide variant (mSNV) analysis during an influenza A/H5N8 outbreak
Marjolein J Poen,Anne Pohlmann,Clara Amid,Theo M. Bestebroer,Sharon M. Brookes,Ian H. Brown,Helen Everett,Claudia M. E. Schapendonk,Rachel D Scheuer,Saskia L. Smits,Martin Beer,Ron A. M. Fouchier,Richard J. Ellis +12 more
TL;DR: This analysis demonstrated that variation in the final result could be attributed to all stages in the process, but the most critical were the well-known homopolymer errors introduced by 454 sequencing, and the alignment processes in the different data processing pipelines which affected the consistency of mSNV detection.
Posted ContentDOI
Shiny-SoSV: A web app for interactive evaluation of somatic structural variant calls
Tingting Gong,Tingting Gong,Vanessa M. Hayes,Vanessa M. Hayes,Vanessa M. Hayes,Eva K. F. Chan,Eva K. F. Chan +6 more
TL;DR: Shiny-SoSV is an interactive web application for evaluating the effects of five common variables on the sensitivity and precision of somatic structural variant calls, thereby enabling users to quickly make informed sequencing and bioinformatics decisions early on in their study design.
Posted ContentDOI
Long reads from Nanopore sequencing as a tool for animal microbiome studies
TL;DR: Compared the performance of both types of sequencing applied to samples of ruminal content using a similar pipeline, the ONT sequencing provided similar results to the Illumina sequencing, although it was able to classify a greater number of readings at the species level, possibly due to the increase in the read size.
The role of read depth in the design and analysis of sequencing experiments
TL;DR: It is shown that per-gene read depth can be taken into account in multiple hypothesis testing to improve power, and introduced the method of functional false discovery rate (fFDR) control.
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.