Automated Scoring of AFLPs Using RawGeno v 2.0, a Free R CRAN Library View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2012-04-24

AUTHORS

Nils Arrigo , Rolf Holderegger , Nadir Alvarez

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. More... »

PAGES

155-175

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-1-61779-870-2_10

DOI

http://dx.doi.org/10.1007/978-1-61779-870-2_10

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1006625244

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/22665281


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