Selection of different scripts that I wrote to handle my PhD data.
I am doing a PhD in plants/pathogens applied bioinformatics. My PhD research have used various datasets for different purposes, including (1) Next Generation Sequencing (NGS) data using DArTseq for analyses such as phylogeny, haplotype blocks, GWAS and (2) Pacbio and Illumina sequencing reads for genome assembly, gene prediction, functional annotation and etc.
When I started my PhD in 2014, I barely knew anything about computational biology and bioinformatics (and I am still learning :) ). I benefited enormously from scripts available online and thanks to the guidance of many wonderful people including my supervisors and colleagues I trained myself in scripting to serve my PhD needs. Although all scripts in here are written based on my data, I hope with sharing it someone else may still find it useful. For the scripts' usage please view the code's comment section. There is an example file in each folder which the code was written based on that.
Yes! I am eternally grateful to many people for my PhD study, but when it comes to scripting special thanks goes to my supervisor Dr Philipp Bayer, who patiently answered my millions of questions and debugged my scripts when I was stuck!