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
Citations
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A survey of best practices for RNA-seq data analysis
Ana Conesa,Pedro Madrigal,Pedro Madrigal,Sonia Tarazona,David Gomez-Cabrero,Alejandra Cervera,Andrew McPherson,Michał Wojciech Szcześniak,Daniel J. Gaffney,Laura L. Elo,Xuegong Zhang,Ali Mortazavi +11 more
TL;DR: All of the major steps in RNA-seq data analysis are reviewed, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping.
Journal ArticleDOI
Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
Etienne Becht,Nicolas A. Giraldo,Nicolas A. Giraldo,Nicolas A. Giraldo,Laetitia Lacroix,Laetitia Lacroix,Laetitia Lacroix,Bénédicte Buttard,Bénédicte Buttard,Bénédicte Buttard,Nabila Elarouci,Florent Petitprez,Janick Selves,Pierre Laurent-Puig,Catherine Sautès-Fridman,Catherine Sautès-Fridman,Catherine Sautès-Fridman,Wolf H. Fridman,Wolf H. Fridman,Wolf H. Fridman,Aurélien de Reyniès +20 more
TL;DR: The Microenvironment Cell Populations-counter method is introduced, which allows the robust quantification of the absolute abundance of eight immune and two stromal cell populations in heterogeneous tissues from transcriptomic data and demonstrates that MCP-counter overcomes several limitations or weaknesses of previously proposed computational approaches.
Journal ArticleDOI
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Donovan H. Parks,Christian Rinke,Maria Chuvochina,Pierre-Alain Chaumeil,Ben J. Woodcroft,Paul N. Evans,Philip Hugenholtz,Gene W. Tyson +7 more
TL;DR: The recovery of 7,903 bacterial and archaeal metagenome-assembled genomes increases the phylogenetic diversity represented by public genome repositories and provides the first representatives from 20 candidate phyla.
Journal ArticleDOI
Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data
TL;DR: Qualimap 2 represents a next step in the QC analysis of HTS data, along with comprehensive single-sample analysis of alignment data, and includes new modes that allow simultaneous processing and comparison of multiple samples.
Journal ArticleDOI
UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy
TL;DR: It is shown that errors in the UMI sequence are common and network-based methods to account for these errors when identifying PCR duplicates are introduced, demonstrating the value of properly accounting for errors in UMIs.
References
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Efficient Study Design for Next Generation Sequencing
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Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence
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Exome RNA sequencing reveals rare and novel alternative transcripts
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Journal ArticleDOI
A mechanistic basis for amplification differences between samples and between genome regions
Colin Veal,Peter Freeman,Kevin B. Jacobs,Owen Lancaster,Stéphane Jamain,Stéphane Jamain,Marion Leboyer,Marion Leboyer,Demetrius Albanes,Reshma R Vaghela,Ivo Gut,Stephen J. Chanock,Anthony J. Brookes +12 more
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High-throughput microbial population genomics using the Cortex variation assembler
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