Humble E, Hosegood J, Carvalho G, de Bruyn M, Creer S, Stevens GMW, Armstrong A, Bonfil R, Deakos M, Fernando D, Froman N, Peel LR, Pollett S, Ponzo A, Stewart JD, Wintner S, Ogden R Comparative population genomics of manta rays has global implications for management. Molecular Ecology. https://doi.org/10.1111/mec.17220
This repository contains the scripts required for all analysis in the paper above. The repository also contains scripts for producing all figures.
For the STACKS and SNP calling and filtering pipeline refer to the /workflows directory. The /scripts directory contains scripts that are called in the main workflow.
Scripts for use in STACKS pipeline
1.0_cat_demultiplexed_files.R
1.1_prep_pop_maps.R
1.2_param_optimisation.R
1.3_get_catalog.R
SNP QC and file preparation
2.0_snp_sumstats.R
2.1_prep_dup_files.R
2.2_error_rate.R
2.3_relatedness.R
3.0_make_files.R
Population structure and gene flow
4.0_PCA_DAPC.R
4.1_admixture_out.R
4.2_map.R
Genetic diversity and downstream treemix
5.0_IBD_dbMEM_RDA.R
5.1_FST_WC.R
6.0_het.R
7.0_ba3.R
8.0_treemix.R
Figure generation
9.0_figures.R
Sequencing reads are available at the European Nucleotide Archive (https://www.ebi.ac.uk/ena/browser) under study accession PRJEB66437.