Abstract
Amplified Fragment Length Polymorphisms (AFLPs) are a cheap and efficient protocol for generating large sets of genetic markers. This technique has become increasingly used during the last decade in various fields of biology, including population genomics, phylogeography, and genome mapping. Here, we present RawGeno, an R library dedicated to the automated scoring of AFLPs (i.e., the coding of electropherogram signals into ready-to-use datasets). Our program includes a complete suite of tools for binning, editing, visualizing, and exporting results obtained from AFLP experiments. RawGeno can either be used with command lines and program analysis routines or through a user-friendly graphical user interface. We describe the whole RawGeno pipeline along with recommendations for (a) setting the analysis of electropherograms in combination with PeakScanner, a program freely distributed by Applied Biosystems; (b) performing quality checks; (c) defining bins and proceeding to scoring; (d) filtering nonoptimal bins; and (e) exporting results in different formats.
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Acknowledgments
We are grateful to Anahi Espindola, Matthias Borer, and Aurélien Labhardt for kindly providing the AFLP datasets presented in Notes 2–4. We thank Nicolas Salamin for having provided a working environment to N. Arrigo during the redaction of this manuscript. Felix Gugerli, Sabine Brodbeck, Piya Kittipadakul, Julie B. Hébert, Julie Lee Yaw, Christian Parisod, Roland Dubillard, and Robin Arnoux provided helpful comments during the development of RawGeno. This project was supported by the National Centre of Competence in Research (NCCR) Plant Survival and the PNR-59, two programs of the Swiss National Science Foundation. N. Alvarez and N. Arrigo were funded by the Swiss National Science Foundation (Ambizione fellowship PZ00P3_126624 and prospective researcher fellowship PBNEP3_132747, respectively).
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Arrigo, N., Holderegger, R., Alvarez, N. (2012). Automated Scoring of AFLPs Using RawGeno v 2.0, a Free R CRAN Library. In: Pompanon, F., Bonin, A. (eds) Data Production and Analysis in Population Genomics. Methods in Molecular Biology, vol 888. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-870-2_10
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DOI: https://doi.org/10.1007/978-1-61779-870-2_10
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