TY - JOUR
T1 - Galaxy tools to study genome diversity
AU - Bedoya-Reina, Oscar C.
AU - Ratan, Aakrosh
AU - Burhans, Richard
AU - Kim, Hie Lim
AU - Giardine, Belinda
AU - Riemer, Cathy
AU - Li, Qunhua
AU - Olson, Thomas L.
AU - Loughran, Thomas P.
AU - vonHoldt, Bridgett Marie
AU - Perry, George H.
AU - Schuster, Stephan C.
AU - Miller, Webb
N1 - Funding Information:
We thank Andreanna Welsh and Charlotte Lindqvist for early testing of the Galaxy tools, Carl-Johan Rubin and Leif Andersson for graciously supplying the chicken data, and Martien Groenen for providing the pig data. The dbSNP on-line help-desk extracted the comments in the chicken SNP entries. Michael DeGiorgio discussed the interplay between admixture and identification of selective sweeps. Development of the Galaxy tools for analyzing SNVs from low-coverage sequence data was supported in part by NIH award 1 UL1 RR033184-01 to the Penn State Clinical and Translational Science Institute, with supplemental funding from a grant from the Pennsylvania Department of Health using Tobacco Commonwealth Universal Research Enhancement Funds. TLO and TPL were supported by NIH award CA 170334. Development of the tools to help guide captive-breeding programs (tools #19-#23) was supported by the Gordon and Betty Moore Foundation, and was helped by suggestions from Katherine Rall and Jon Ballou.
Publisher Copyright:
© 2013 Bedoya-Reina et al.
PY - 2013
Y1 - 2013
N2 - 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.
AB - 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.
KW - Admixture
KW - Genome analysis
KW - Population structure
KW - Selective sweeps
KW - Species conservation
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U2 - 10.1186/2047-217X-2-17
DO - 10.1186/2047-217X-2-17
M3 - Article
C2 - 24377391
AN - SCOPUS:84991529239
SN - 2047-217X
VL - 2
JO - GigaScience
JF - GigaScience
IS - 1
M1 - 17
ER -