Galaxy tools to study genome diversity

Oscar C. Bedoya-Reina, Aakrosh Ratan, Richard Burhans, Hie Lim Kim, Belinda Giardine, Cathy Riemer, Qunhua Li, Thomas L. Olson, Thomas P. Loughran, Bridgett Marie vonHoldt, George H. Perry, Stephan C. Schuster, Webb Miller

Research output: Contribution to journalArticle

15 Scopus citations

Abstract

Background: Intra-species genetic variation can be used to investigate population structure, selection, and gene flow in non-model vertebrates; and due to the plummeting costs for genome sequencing, it is now possible for small labs to obtain full-genome variation data from their species of interest. However, those labs may not have easy access to, and familiarity with, computational tools to analyze those data. Results: We have created a suite of tools for the Galaxy web server aimed at handling nucleotide and amino-acid polymorphisms discovered by full-genome sequencing of several individuals of the same species, or using a SNP genotyping microarray. In addition to providing user-friendly tools, a main goal is to make published analyses reproducible. While most of the examples discussed in this paper deal with nuclear-genome diversity in non-human vertebrates, we also illustrate the application of the tools to fungal genomes, human biomedical data, and mitochondrial sequences. Conclusions: This project illustrates that a small group can design, implement, test, document, and distribute a Galaxy tool collection to meet the needs of a particular community of biologists.

Original languageEnglish (US)
Article number17
JournalGigaScience
Volume2
Issue number1
DOIs
StatePublished - Jan 1 2013

All Science Journal Classification (ASJC) codes

  • Computer Science Applications
  • Health Informatics

Keywords

  • Admixture
  • Genome analysis
  • Population structure
  • Selective sweeps
  • Species conservation

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  • Cite this

    Bedoya-Reina, O. C., Ratan, A., Burhans, R., Kim, H. L., Giardine, B., Riemer, C., Li, Q., Olson, T. L., Loughran, T. P., vonHoldt, B. M., Perry, G. H., Schuster, S. C., & Miller, W. (2013). Galaxy tools to study genome diversity. GigaScience, 2(1), [17]. https://doi.org/10.1186/2047-217X-2-17