GigaGalaxy workflows and histories from “Galaxy tools to study genome diversity”

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.
A suite of tools for the Galaxy web server have been created 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. These tools are presented in a GigaScience publication (doi: 10.1186/2047-217X-2-17), and in order to facilitate readers to repeat and recreate the examples given in the paper, we present here the pipelines and histories, both accessible from our GigaGalaxy server, and as Galaxy XML files available to download. The five workflows included relate to examples in the paper dealing with nuclear-genome diversity in non-human vertebrates, and also illustrate the application of the tools to fungal genomes, human biomedical data, and mitochondrial sequences.

Read the peer-reviewed publication(s):

• 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). https://doi.org/10.1186/2047-217x-2-17

Additional information:

http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/g/obedoyareina2013