Microarrays can be a cost-effective alternative to high-throughput sequencing for discovering novel single-nucleotide polymorphisms (SNPs). Illumina’s iScan platform dominates the market, but their commercial microarray products are designed for model organisms. Further, the platform outputs data in a proprietary format. This cannot be easily converted to human-readable genotypes or be merged with pre-existing data. To address this, we present and validate a novel pipeline to facilitate data analysis from cross-species application of Illumina microarrays. This facilitates the generation of a compatible VCF from iScan data and the merging of this with a second VCF comprising genotypes derived from other samples and sources. Our pipeline includes a custom script, iScanVCFMerge (presented as a Python package), which we validate using iScan data from three great ape genera. We conclude that cross-species application of microarrays can be a rapid, cost-effective approach for SNP discovery in non-model organisms. Our pipeline surmounts the common challenges of integrating iScan genotypes with pre-existing data.
CITATION STYLE
Fountain, E. D., Zhou, L. C., Karklus, A., Liu, Q. X., Meyers, J., Fontanilla, I. K. C., … Banes, G. L. (2021). Cross-Species Application of Illumina iScan Microarrays for Cost-Effective, High-Throughput SNP Discovery. Frontiers in Ecology and Evolution, 9. https://doi.org/10.3389/fevo.2021.629252
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