Haemonchus_diversity

Code and data for global diversity study.

These scripts are distributed in the hope that they will be useful, but WITHOUT ANY WARRANTY.

Main script

GlobalDiversityScript.R : R script used to analyse the data and produce figures and supplementary figures.

Helper scripts

These are a few tools used to create intermediate files needed in GlobalDiversityScript.R.

• convert_hits_to_gene.sh: A shell script needed to convert v3 assembly coordinates into v0 assembly gene identifier. This script uses a python script (split_ref_by_contigs.py) and another shell for interecting bed file with gtf (retrieve_gene_gtf_from_blast.sh).

• create_GradientForest_input_ANGSD.py : A python script to combine minor allele frequency estimates from ANGSD with environmental data into an input file needed for gradientForest analysis.

• bootstrap.py : A python script to estimate parameter uncertainty using a Godambe Information Matrix with dadi (inspired from Peter Beerli's code: http://www.peterbeerli.com/classes/index.php?title=DadiTutorial).

This work is licensed under a Creative Commons Attribution 4.0 International License.