Sequence analysis

Analyses of sequences

Requirements

Before diving into this topic, we recommend you to have a look at:

• Introduction to Galaxy Analyses

Material

The Basics

These tutorials cover basic operations common to many sequence-bases analyses

Other

Assorted Tutorials

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.

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Community Resources

Editorial Board

This material is reviewed by our Editorial Board:

Yvan Le Bras

Bérénice Batut

Joachim Wolff

Are you on the editorial board or want to help out with this topic? View the topic maintainer page for ways to improve this topic!

Contributors

This material was contributed to by:

Nicola Soranzo

Coline Royaux

Alexandre Cormier

Anne Fouilloux

Verena Moosmann

Eric Tvedte

Saskia Hiltemann

Joachim Wolff

Anthony Bretaudeau

Bérénice Batut

Helena Rasche

Tristan Reynolds

Niall Beard

Elischa Berger

Ekaterina Polkh

Robert Meller

Maria Doyle

Anika Erxleben

Deepti Varshney

Mateo Boudet

Ava Hoffman

Björn Grüning

Laura Leroi

Stéphanie Robin

Cristóbal Gallardo

Natalie Kucher

Mehmet Tekman

Swathi Nataraj

Frederick Tan

Simon Bray

Elizabeth Humphries

William Durand

Katherine Cox

Erwan Corre

Cameron Hyde

Clea Siguret

Candace Savonen

Wolfgang Maier

Matthias Bernt

Anup Kumar

Teresa Müller

Funding

These individuals or organisations provided funding support for the development of this resource

NIH

Australian BioCommons

NHGRI ANVIL

MAdLand

NHGRI GDS Community Network

Gallantries

This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.

The University of Melbourne

ABRomics

DataPLANT

BeYond-COVID

BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response. This project has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement № 101046203 (BY-COVID)

Melbourne Bioinformatics

References

• 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
  
• Catchen, J. M. et al. 2011: Stacks: building and genotyping loci de novo from short-read sequences
  
• Davey, J. W., et al. 2011: Genome-wide genetic marker discovery and genotyping using next-generation sequencing
  
• Etter, P. D., et al. 2011: SNP Discovery and Genotyping for Evolutionary Genetics using RAD sequencing
  
• Ekblom, R., and J. Galindo. 2010: Applications of next generation sequencing in molecular ecology of non-model organisms
  
• Hohenlohe, P. A. et al. 2010: Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags
  
• Gompert, Z., and C. A. Buerkle. 2011a: A hierarchical Bayesian model for next-generation population genomics
  
• Gompert, Z., and C. A. Buerkle. 2011b: Bayesian estimation of genomic clines
  
• Lynch, M. 2009: Estimation of allele frequencies from high-coverage genome-sequencing projects
  
• Nielsen, R., et al. 2005: Genomic scans for selective sweeps using SNP data
  
• Hohenlohe, P. A., et al. 2010: Using population genomics to detect selection in natural populations: Key concepts and methodological considerations
  
• Stapley, J., et al. 2010: Adaptation genomics: the next generation
  
• Altshuler, D., et al. 2000: An SNP map of the human genome generated by reduced representation shotgun sequencing
  
• Baxter, S. W., et al. 2011: Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism
  
• Chutimanitsakun, Y., et al. 2011: Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley
  
• Gore, M. A., et al. 2009: A first-generation haplotype map of maize
  
• Baird, N. A., et al. 2008: Rapid SNP discovery and genetic mapping using sequenced RAD markers
  
• Emerson, K. J., et al. 2010: Resolving postglacial phylogeography using high-throughput sequencing
  
• Etter, P. D., et al. 2011: Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads
  
• Hohenlohe, P. A., et al. 2011: Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout
  
• Miller, M. R., et al. 2007: Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers
  
• Willing, E. M., et al. 2011: Paired-end RAD-seq for de novo assembly and marker design without available reference
  
• Andolfatto, P., et al. 2011: Multiplexed shotgun genotyping for rapid and efficient genetic mapping
  
• Elshire, R. J., et al. 2011: A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
  
• Rigola, D., et al. 2009: High-Throughput Detection of Induced Mutations and Natural Variation Using KeyPoint™ Technology
  
• van Orsouw, N. J., et al. 2007: Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes
  
• van Tassell, C. P., et al. 2008: SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
  
• Luikart, G.,et al. 2003: The power and promise of population genomics: from genotyping to genome typing
  
• Nielsen, R., et al. 2011: Genotype and SNP calling from next-generation sequencing data