Galaxy tools to study genome diversity
1 Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA
2 Terreus Foundation, 3938 Trust Way, Hayward, CA 94545, USA
3 Penn State Hershey Cancer Institute, Hershey, PA 17033, USA
4 Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
5 Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
GigaScience 2013, 2:17 doi:10.1186/2047-217X-2-17Published: 30 December 2013
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.
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.
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.