Lonsinger, R. C., and L. P. Waits. 2015. ConGenR: rapid determination of consensus genotypes and estimates of genotyping errors from replicated genetic samples. Conservation Genetics Resources 7:841–843. doi: 10.1007/s12686-015-0506-7.
ConGenR (available at http://www.uidaho.edu/cnr/research-outreach/facilities/leecg/publications-and-software) is an R based conservation genetics script that facilitates rapid determination of consensus genotypes from replicated samples, determines overall (successful amplifications/amplification attempted) and individual sample level (proportion of samples with successful amplifications at n loci) amplification success rates, and quantifies genotyping error rates. ConGenR is intended for use with codominant, multilocus microsatellite data generated primarily through noninvasive genetic sampling and processed with a multi-tubes approach. ConGenR handles input that can be easily exported from GENEMAPPER, a program commonly used to score allele sizes. Amplification success and genotyping error rates can be evaluated by sample class (i.e., any identifiable and meaningful subdivision of samples; e.g., sex, season, region, or sample condition), offering insights into processes driving amplification success and genotyping error rates. Additionally, amplification success and genotyping error rates are calculated by locus, expediting the identification of problematic loci during pilot studies.