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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Brazilian forensic casework analysis through MPS applications: Statistical weight-of-evidence and biological nature of criminal samples as an influence factor in quality metrics.
Eduardo Avila,C.P. Cavalheiro,Aline B. Felkl,Pietra Graebin,Alessandro Kahmann,Clarice Sampaio Alho +5 more
TL;DR: This study analyzes a set of 47 real forensic casework samples, obtained from semen, saliva, blood and epithelial evidence, as well as reference oral swabs, aiming to evaluate the impact of a sample's biological nature in profiling success, and indicates that a unified national allele frequency database can be used nationwide.
Journal ArticleDOI
A European-wide dataset to uncover adaptive traits of Listeria monocytogenes to diverse ecological niches
Benjamin Félix,Yann Sévellec,Federica Palma,Pierre-Emmanuel Douarre,Arnaud Felten,Nicolas Radomski,Ludovic Mallet,Yannick Blanchard,A Leroux,C. Soumet,Arnaud Bridier,Pascal Piveteau,Eliette Ascensio,Michel Hébraud,Renata Karpíšková,Tereza Gelbíčová,Marina Torresi,Francesco Pomilio,Cesare Cammà,Adriano Di Pasquale,Taran Skjerdal,Ariane Pietzka,Werner Ruppitsch,Monica Ricão Canelhas,Bojan Papić,Ana Hurtado,Bart A. Wullings,Hana Bulawová,Hanna Castro,Miia Lindström,Hannu Korkeala,Zanete Steingolde,Toomas Kramarenko,L. Cabanová,Barbara Szymczak,Manfred Gareis,Verena Oswaldi,Elisabet Marti,Anne Mette Seyfarth,Jean-Charles Leblanc,Laurent Greillier,Sophie Roussel +41 more
TL;DR: In this article , a dataset of 1484 genomes from Listeria monocytogenes (Lm) strains collected in 19 European countries is presented, covering many diverse habitats and balanced between ecological compartments and geographic regions.
Journal ArticleDOI
Challenges in the application of NGS in the clinical laboratory.
TL;DR: In this paper, the authors examined the role of NGS technologies in clinical immunology for HLA genotyping and discussed the challenges of next-generation sequencing implementation in clinical laboratories.
Secuenciación y ensamblaje de novo de genomas bacterianos: una alternativa para el estudio de nuevos patógenos
TL;DR: The main trends regarding sequencing, and specifically the de novo assembly, are reviewed and the approaches used to reconstruct genomes, particularly bacterial genomes are reviewed.
Posted ContentDOI
Comparative metaproteomics demonstrates different views on the complex granular sludge microbiome
Hugo B.C. Kleikamp,Dennis Grouzdev,Pim Schaasberg,Ramon van Valderen,Ramon van der Zwaan,Roel van de Wijgaart,Yuemei Lin,Ben Abbas,Mario Pronk,M.C.M. van Loosdrecht,Martin Pabst +10 more
TL;DR: A deep, comparative metaproteomic study on the complex aerobic granular sludge microbiome obtained from different wastewater treatment plants is described and a ‘homogenized’ Genome Taxonomy Database (GTDB) is demonstrated that enables a more accurate interpretation of data from different omics approaches.
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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.