Assessing ancestry of North American honey bees (Apis mellifera) through low-pass whole-genome sequencing

Important Files

ahb_pipeline_v2.sh
- full bash script to run ancestry analysis and PCA using imputed data
unimpt.sh
- version of above taking only observed genotypes (uses no imputation)
n_mitotype.sh
- full bash script to run mitotyping analysis
aimIa_v2.R
- custom R script to caluclate site informativeness for ancestry
ahb_analysis.R
- analyses included in publication, including logistic regression, PCA, and ancestry figures
corr_concordance.cpp
- This C++ program used to estimate correlation and concordance rate between imputed and observed genotype for a large-dimenssional dataset. The code will generate a dataframe of concordance rate and imputation accuracy.
recombRate.R
- custom R script to calculate recombination rate

Name		Name	Last commit message	Last commit date
Latest commit History 78 Commits
aim		aim
outputs		outputs
references		references
.gitignore		.gitignore
1_array_filter_v3.sh		1_array_filter_v3.sh
AHB_markers.fasta		AHB_markers.fasta
AHB_markers_FL.fasta		AHB_markers_FL.fasta
AIM_v3.sh		AIM_v3.sh
LDprune_p.R		LDprune_p.R
README.md		README.md
ahb_analysis.R		ahb_analysis.R
ahb_metadata.csv		ahb_metadata.csv
ahb_pipeline_v3.sh		ahb_pipeline_v3.sh
aimIa_v2.R		aimIa_v2.R
corr_concord.cpp		corr_concord.cpp
makeAdmixPop.R		makeAdmixPop.R
n_mitotype.sh		n_mitotype.sh
prune_array.sh		prune_array.sh
recombRate.R		recombRate.R
refData.txt		refData.txt
sentinel.txt		sentinel.txt
sra_upload.sh		sra_upload.sh
supervised_admix_v3.sh		supervised_admix_v3.sh
unarchive_cmd2.txt		unarchive_cmd2.txt
unimpt.sh		unimpt.sh
unsupervised_v3.sh		unsupervised_v3.sh
zip.sh		zip.sh