Scripts related to Forsdick (2020), 'Assessment of the impacts of anthropogenic hybridisation in a threatened non-model bird species through the development of genomic resources with implications for conservation,' PhD thesis associated with interspecific hybridisation between kakī (Himantopus novaezelandiae) and poaka (Himantopus himantopus leucocephalus). Thesis permanent link: http://hdl.handle.net/10523/10268.
Associated peer-reviewed publications:
- Galla, Forsdick et al. (2019). Reference Genomes from Distantly Related Species Can Be Used for Discovery of Single Nucleotide Polymorphisms to Inform Conservation Management. Genes, 10(1), 9. https://doi.org/10.3390/genes10010009.
- Forsdick et al. (2021).Genomic sequencing confirms absence of introgression despite past hybridisation between a critically endangered bird and its common congener. Global Ecology and Conservation, 28, e01681. https://doi.org/10.1016/j.gecco.2021.e01681.
Raw_read_QC_trim.sh is a script for performing quality control for short-read whole genome sequencing data. It uses FastQC to assess raw read quality, Trimmomatic for adapter removal, and ConDeTri for quality trimming and read deduplication.
Streamlined_GBS_pipeline.md describes a straightforward analysis pipeline for GBS data including demultiplexing, mapping, variant discovery and filtering, and additional pre-processing prior to analysis with ADMIXTURE and/or adegenet.
admixture_array_nesi.sh is a SLURM array script to run ADMIXTURE, with ten iterations for each value of K from 1 - 10.
pophelper-analysis.Rmd is an Rmarkdown script to merge and visualise the results of multiple iterations of ADMIXTURE analysis.
Forsdick-et-al_Stilts_SNPRelate.Rmd includes the methods used to perform population clustering, and estimation of relatedness and Fst using the R package SNPRelate. The results of this analysis are appended as Supplementary File 1 in Forsdick et al., 2021.