Sequence analysis
Analyses of sequences
You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.Requirements
Before diving into this topic, we recommend you to have a look at:
Material
Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows | Galaxy servers |
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Mapping
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Quality Control
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Removal of human reads from SARS-CoV-2 sequencing data | tutorial Toggle Dropdown |
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Galaxy instances
You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.
You can also use the following Docker image for these tutorials:
docker run -p 8080:80 quay.io/galaxy/sequence-analysis-training
NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.
It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.
Frequently Asked Questions
Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.Maintainers
This material is maintained by:
Yvan Le Bras Bérénice Batut Joachim WolffFor any question related to this topic and the content, you can contact them or visit our Gitter channel.
Contributors
This material was contributed to by:
Joachim Wolff Bérénice Batut Helena Rasche Maria Doyle Alexandre Cormier Anthony Bretaudeau Laura Leroi Erwan Corre Stéphanie Robin Erasmus+ Programme Wolfgang MaierReferences
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SciLifeLab: QCFAIL
Articles about common next-generation sequencing problems -
Marco-Antonio Mendoza-Parra et al: A quality control system for profiles obtained by ChIP sequencing
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. -
Ana Conesa et al: A survey of best practices for RNA-seq data analysis
Highlights the challenges associated with each step of RNA-seq data analysis. -
Yuval Benjamini et al: Summarizing and correcting the GC content bias in high-throughput sequencing
Summarizes the many possible sourced of GC bias for deeply sequenced samples. -
David Sims et al: Sequencing depth and coverage: key considerations in genomic analyses
Discuss the issue of sequencing depth in the design of next-generation sequencing experiments. -
Frontiers in Genetics: Quality assessment and control of high-throughput sequencing data
Collection of papers on quality controls for various NGS applications -
Frazer Meacham et al: Identification and correction of systematic error in high-throughput sequence data
Reviews and proposes correction for systematic base pair errors in deep sequencing -
Guillaume Devailly et al: Heat seq: an interactive web tool for high-throughput sequencing experiment comparison with public data
Presents a web-tool that allows genome scale comparison of high throughput experiments -
Amores, A., et al. 2011: Genome evolution and meiotic maps by massively parallel DNA sequencing
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Catchen, J. M. et al. 2011: Stacks: building and genotyping loci de novo from short-read sequences
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Davey, J. W., et al. 2011: Genome-wide genetic marker discovery and genotyping using next-generation sequencing
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Etter, P. D., et al. 2011: SNP Discovery and Genotyping for Evolutionary Genetics using RAD sequencing
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Ekblom, R., and J. Galindo. 2010: Applications of next generation sequencing in molecular ecology of non-model organisms
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Hohenlohe, P. A. et al. 2010: Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags
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Gompert, Z., and C. A. Buerkle. 2011a: A hierarchical Bayesian model for next-generation population genomics
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Gompert, Z., and C. A. Buerkle. 2011b: Bayesian estimation of genomic clines
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Lynch, M. 2009: Estimation of allele frequencies from high-coverage genome-sequencing projects
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Nielsen, R., et al. 2005: Genomic scans for selective sweeps using SNP data
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Hohenlohe, P. A., et al. 2010: Using population genomics to detect selection in natural populations: Key concepts and methodological considerations
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Stapley, J., et al. 2010: Adaptation genomics: the next generation
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Altshuler, D., et al. 2000: An SNP map of the human genome generated by reduced representation shotgun sequencing
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Baxter, S. W., et al. 2011: Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism
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Chutimanitsakun, Y., et al. 2011: Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley
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Gore, M. A., et al. 2009: A first-generation haplotype map of maize
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Baird, N. A., et al. 2008: Rapid SNP discovery and genetic mapping using sequenced RAD markers
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Emerson, K. J., et al. 2010: Resolving postglacial phylogeography using high-throughput sequencing
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Etter, P. D., et al. 2011: Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads
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Hohenlohe, P. A., et al. 2011: Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout
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Miller, M. R., et al. 2007: Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers
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Willing, E. M., et al. 2011: Paired-end RAD-seq for de novo assembly and marker design without available reference
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Andolfatto, P., et al. 2011: Multiplexed shotgun genotyping for rapid and efficient genetic mapping
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Elshire, R. J., et al. 2011: A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
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Rigola, D., et al. 2009: High-Throughput Detection of Induced Mutations and Natural Variation Using KeyPoint™ Technology
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van Orsouw, N. J., et al. 2007: Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes
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van Tassell, C. P., et al. 2008: SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
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Luikart, G.,et al. 2003: The power and promise of population genomics: from genotyping to genome typing
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Nielsen, R., et al. 2011: Genotype and SNP calling from next-generation sequencing data