2007: Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes 2009: High-Throughput Detection of Induced Mutations and Natural Variation Using KeyPoint™ Technology 2011: A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species 2011: Multiplexed shotgun genotyping for rapid and efficient genetic mapping 2011: Paired-end RAD-seq for de novo assembly and marker design without available reference 2007: Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers 2011: Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout 2011: Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads 2010: Resolving postglacial phylogeography using high-throughput sequencing 2008: Rapid SNP discovery and genetic mapping using sequenced RAD markers 2009: A first-generation haplotype map of maize 2011: Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley 2011: Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism 2000: An SNP map of the human genome generated by reduced representation shotgun sequencing 2010: Adaptation genomics: the next generation 2010: Using population genomics to detect selection in natural populations: Key concepts and methodological considerations 2005: Genomic scans for selective sweeps using SNP data 2009: Estimation of allele frequencies from high-coverage genome-sequencing projects 2011b: Bayesian estimation of genomic clines 2011a: A hierarchical Bayesian model for next-generation population genomics 2010: Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags 2010: Applications of next generation sequencing in molecular ecology of non-model organisms 2011: SNP Discovery and Genotyping for Evolutionary Genetics using RAD sequencing 2011: Genome-wide genetic marker discovery and genotyping using next-generation sequencing 2011: Stacks: building and genotyping loci de novo from short-read sequences 2011: Genome evolution and meiotic maps by massively parallel DNA sequencing Presents a web-tool that allows genome scale comparison of high throughput experiments Guillaume Devailly et al: Heat seq: an interactive web tool for high-throughput sequencing experiment comparison with public data.Reviews and proposes correction for systematic base pair errors in deep sequencing Frazer Meacham et al: Identification and correction of systematic error in high-throughput sequence data.Frontiers in Genetics: Quality assessment and control of high-throughput sequencing dataĬollection of papers on quality controls for various NGS applications.David Sims et al: Sequencing depth and coverage: key considerations in genomic analysesĭiscuss the issue of sequencing depth in the design of next-generation sequencing experiments.Summarizes the many possible sourced of GC bias for deeply sequenced samples. Yuval Benjamini et al: Summarizing and correcting the GC content bias in high-throughput sequencing.Highlights the challenges associated with each step of RNA-seq data analysis. Ana Conesa et al: A survey of best practices for RNA-seq data analysis.Presents an approach that associates global and local QC indicators to ChIP-seq data sets as well as to a variety of enrichment-based studies by NGS. Marco-Antonio Mendoza-Parra et al: A quality control system for profiles obtained by ChIP sequencing.This material was contributed to by: Wolfgang Maier Helena Rasche Alexandre Cormier Laura Leroi Joachim Wolff Stéphanie Robin Anthony Bretaudeau Maria Doyle Bérénice Batut Erwan Corre Deepti Varshney Erasmus+ Programme ReferencesĪrticles about common next-generation sequencing problems This material is maintained by: Yvan Le Bras Bérénice Batut Joachim Wolffįor any question related to this topic and the content, you can contact them or visit our Gitter channel. Common questions related to specific tutorials can be accessed from the tutorials themselves. Frequently Asked QuestionsĬommon questions regarding this topic have been collected on a dedicated FAQ page. Login as admin with password password to access everything. It will launch a flavored Galaxy instance available on This instance will contain all the tools and workflows to follow the tutorials in this topic. NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container. Docker run -p 8080:80 quay.io/galaxy/sequence-analysis-training
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