Document Type
Article
Publication Date
1-2023
Keywords
Genetics; Population analysis; AdmixPipe
Abstract
Quantifying genetic clusters (=populations) from genotypic data is a fundamental, but non-trivial task for population geneticists that is compounded by: hierarchical population structure, diverse analytical methods, and complex software dependencies. AdmixPipe v3 ameliorates many of these issues in a single bioinformatic pipeline that facilitates all facets of population structure analysis by integrating outputs generated by several popular packages (i.e. CLUMPAK, EvalAdmix). The pipeline interfaces disparate software packages to parse Admixture outputs and conduct EvalAdmix analyses in the context of multimodal population structure results identified by CLUMPAK. We further streamline these tasks by packaging AdmixPipe v3 within a Docker container to create a standardized analytical environment that allows for complex analyses to be replicated by different researchers. This also grants operating system flexibility and mitigates complex software dependencies.
Citation
Mussmann, S. M., Douglas, M. R., Chafin, T., & Douglas, M. E. (2023). AdmixPipe v3: facilitating population structure delimitation from SNP data. Bioinformatics Advances, 3 (1), vbad168. https://doi.org/10.1093/bioadv/vbad168
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
