--- name: "sequence-analysis" type: "use" topic_type: technology title: "Sequence analysis" summary: "Analyses of sequences" edam_ontology: ["topic_0080"] docker_image: "quay.io/galaxy/sequence-analysis-training" requirements: - type: "internal" topic_name: introduction editorial_board: - yvanlebras - bebatut - joachimwolff subtopics: - id: basics title: "The Basics" description: "These tutorials cover basic operations common to many sequence-bases analyses" references: - authors: "SciLifeLab" title: "QCFAIL" link: "https://sequencing.qcfail.com/" summary: "Articles about common next-generation sequencing problems" - authors: "Marco-Antonio Mendoza-Parra et al" title: "A quality control system for profiles obtained by ChIP sequencing" link: "http://nar.oxfordjournals.org/content/41/21/e196.short" summary: "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." - authors: "Ana Conesa et al" title: "A survey of best practices for RNA-seq data analysis" link: "http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8" summary: "Highlights the challenges associated with each step of RNA-seq data analysis." - authors: "Yuval Benjamini et al" title: "Summarizing and correcting the GC content bias in high-throughput sequencing" link: "http://nar.oxfordjournals.org/content/40/10/e72.long" summary: "Summarizes the many possible sourced of GC bias for deeply sequenced samples." - authors: "David Sims et al" title: "Sequencing depth and coverage: key considerations in genomic analyses" link: "http://www.nature.com/nrg/journal/v15/n2/abs/nrg3642.html" summary: "Discuss the issue of sequencing depth in the design of next-generation sequencing experiments." - authors: "Frontiers in Genetics" title: "Quality assessment and control of high-throughput sequencing data" link: "http://journal.frontiersin.org/researchtopic/1683/quality-assessment-and-control-of-high-throughput-sequencing-data" summary: "Collection of papers on quality controls for various NGS applications" - authors: "Frazer Meacham et al" title: "Identification and correction of systematic error in high-throughput sequence data" link: "http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-451" summary: "Reviews and proposes correction for systematic base pair errors in deep sequencing" - authors: "Guillaume Devailly et al" title: "Heat seq: an interactive web tool for high-throughput sequencing experiment comparison with public data" link: "http://biorxiv.org/content/early/2016/04/18/049254.abstract" summary: "Presents a web-tool that allows genome scale comparison of high throughput experiments" - authors: "Amores, A., et al. 2011" title: "Genome evolution and meiotic maps by massively parallel DNA sequencing" link: "https://www.ncbi.nlm.nih.gov/pubmed/21828280" - authors: "Catchen, J. M. et al. 2011" title: "Stacks: building and genotyping loci de novo from short-read sequences" link: "http://www.g3journal.org/content/1/3/171.full" - authors: "Davey, J. W., et al. 2011" title: "Genome-wide genetic marker discovery and genotyping using next-generation sequencing" link: "https://www.ncbi.nlm.nih.gov/pubmed/21681211" - authors: "Etter, P. D., et al. 2011" title: "SNP Discovery and Genotyping for Evolutionary Genetics using RAD sequencing" link: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3658458/" - authors: "Ekblom, R., and J. Galindo. 2010" title: "Applications of next generation sequencing in molecular ecology of non-model organisms" link: "https://www.ncbi.nlm.nih.gov/pubmed/21139633" - authors: "Hohenlohe, P. A. et al. 2010" title: "Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags" link: "http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000862" - authors: "Gompert, Z., and C. A. Buerkle. 2011a" title: "A hierarchical Bayesian model for next-generation population genomics" link: "http://www.genetics.org/content/187/3/903" - authors: "Gompert, Z., and C. A. Buerkle. 2011b" title: "Bayesian estimation of genomic clines" link: "http://onlinelibrary.wiley.com/wol1/doi/10.1111/j.1365-294X.2011.05074.x/abstract" - authors: "Lynch, M. 2009" title: "Estimation of allele frequencies from high-coverage genome-sequencing projects" link: "http://www.genetics.org/content/182/1/295" - authors: "Nielsen, R., et al. 2005" title: "Genomic scans for selective sweeps using SNP data" link: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1310644/" - authors: "Hohenlohe, P. A., et al. 2010" title: "Using population genomics to detect selection in natural populations: Key concepts and methodological considerations" link: "https://www.ncbi.nlm.nih.gov/pubmed/21218185" - authors: "Stapley, J., et al. 2010" title: "Adaptation genomics: the next generation" link: "http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(10)00216-8" - authors: "Altshuler, D., et al. 2000" title: "An SNP map of the human genome generated by reduced representation shotgun sequencing" link: "https://www.ncbi.nlm.nih.gov/pubmed/11029002" - authors: "Baxter, S. W., et al. 2011" title: "Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism" link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019315" - authors: "Chutimanitsakun, Y., et al. 2011" title: "Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley" link: "http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-4" - authors: "Gore, M. A., et al. 2009" title: "A first-generation haplotype map of maize" link: "http://science.sciencemag.org/content/326/5956/1115" - authors: "Baird, N. A., et al. 2008" title: "Rapid SNP discovery and genetic mapping using sequenced RAD markers" link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003376" - authors: "Emerson, K. J., et al. 2010" title: "Resolving postglacial phylogeography using high-throughput sequencing" link: "http://www.pnas.org/content/107/37/16196" - authors: "Etter, P. D., et al. 2011" title: "Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads" link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018561" - authors: "Hohenlohe, P. A., et al. 2011" title: "Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout" link: "https://www.ncbi.nlm.nih.gov/pubmed/21429168" - authors: "Miller, M. R., et al. 2007" title: "Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers" link: "https://www.ncbi.nlm.nih.gov/pubmed/17189378" - authors: "Willing, E. M., et al. 2011" title: "Paired-end RAD-seq for de novo assembly and marker design without available reference" link: "https://www.ncbi.nlm.nih.gov/pubmed/21712251" - authors: "Andolfatto, P., et al. 2011" title: "Multiplexed shotgun genotyping for rapid and efficient genetic mapping" link: "https://www.ncbi.nlm.nih.gov/pubmed/21233398" - authors: "Elshire, R. J., et al. 2011" title: "A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species" link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019379" - authors: "Rigola, D., et al. 2009" title: "High-Throughput Detection of Induced Mutations and Natural Variation Using KeyPoint™ Technology" link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0004761" - authors: "van Orsouw, N. J., et al. 2007" title: "Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes" link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001172" - authors: "van Tassell, C. P., et al. 2008" title: "SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries" link: "https://www.ncbi.nlm.nih.gov/pubmed/18297082" - authors: "Luikart, G.,et al. 2003" title: "The power and promise of population genomics: from genotyping to genome typing" link: "https://www.ncbi.nlm.nih.gov/pubmed/14631358" - authors: "Nielsen, R., et al. 2011" title: "Genotype and SNP calling from next-generation sequencing data" link: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3593722/"