Software and Guides

Software

PedSam – software to help identify subsets of individuals in a population whose molecular data may be most informative for completing the population pedigree. Windows OS.

CASC (Calculate Allele Sharing Coefficients) – provides an intuitive user interface to calculate pairwise allele sharing coefficients from diploid genotype data (intended for SNPs but works for microsatellites too). Genepop input file. Windows OS.

Guides

Standardized Data Collection Guide –

A guide to the collection of genomic data for improved management of AZA’s living collections. Includes guidance for standardized collection and storing of samples, extracting high quality DNA, mitigating batch effects, and collecting robust sequence data for SNP discovery.

 

 

 

 

Standardized Data Analysis Guide –

A guide to the analysis of genomic data for improved management of AZA’s breeding programs. Provides guidance on best practices for storing sequence data, computing options, Stacks protocols including a wrapper code designed to facilitate implementation, filtering and formatting genotype data, and calculating allele sharing coefficients (using CASC software).