embark-research

Repository of code used in Embark publications.

Table of Contents

2020

Sams, Aaron J, Ford, Brett, Gardner, Adam, and Boyko, Adam R. "Examination of the efficacy of small genetic panels in genomic conservation of companion animal populations." Evolutionary Applications. (In revision - ADD METADATA WHEN PUBLISHED)

• analyze_data_and_make_figures_and_tables.py - A python (3) (we used 3.7.4 at runtime) script to aggregate and analyze raw data from simulation outputs.
• requirements.txt - List of versions of non-standard library python packages used in analyze_data_and_make_figures_and_tables.py
• diversity_matechoice_template_for_manuscript.slim - A template for SLIM 3 used to generate all simulations in this manuscript.

To generate summary stats and build figures and tables (replicate data in manuscript)...

python analyze_data_and_make_figures_and_tables.py 
    --output-root-directory {path_to_output_directory} 
    --simulation-results-root-directory {path_to_unzipped_raw_data} 
    --get-data-from-results-files

Supplementary materials are available with the online version of this manuscript # will add when final version is available Raw simulation data is available on DRYAD

2019

Sams, Aaron J, and Adam R Boyko. “Fine-Scale Resolution of Runs of Homozygosity Reveal Patterns of Inbreeding and Substantial Overlap with Recessive Disease Genotypes in Domestic Dogs.” G3: Genes|Genomes|Genetics, November 14, 2018, g3.200836.2018–7. doi:10.1534/g3.118.200836.

• postprocess_germline.py - A python script with post-processing algorithm for filling gaps and filtering on marker counts in merged homozygosity tracts from germline (1.5.1) using --bits 1.

All other supplementary materials are available at figshare