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Galaxy tools to study genome diversity

Author(s): Bedoya-Reina, Oscar C.; Ratan, Aakrosh; Burhans, Richard; Kim, Hie Lim; Giardine, Belinda; et al

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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.
Publication Date: Dec-2013
Electronic Publication Date: 30-Dec-2013
Citation: Bedoya-Reina, Oscar C, Ratan, Aakrosh, Burhans, Richard, Kim, Hie Lim, Giardine, Belinda, Riemer, Cathy, Li, Qunhua, Olson, Thomas L, Loughran, Thomas P, vonHoldt, Bridgett M, Perry, George H, Schuster, Stephan C, Miller, Webb. (2013). Galaxy tools to study genome diversity. GigaScience, 2 (1), 10.1186/2047-217X-2-17
DOI: doi:10.1186/2047-217X-2-17
EISSN: 2047-217X
Pages: 1 - 20
Type of Material: Journal Article
Journal/Proceeding Title: GigaScience
Version: Final published version. This is an open access article.

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