This is part of a thesis entitled "Aligning with Complexity: Resolving Difficult-to-Detect Genomic Alterations in Acute Lymphoblastic Leukaemia through Pan-Genome Graphs and Optimised Gene Fusion Calling" submitted for the degree of Doctor of Philosophy, by Ashlee Thomson-Roberts.
Scripts for analysis of ALL patient samples using the ALL-specific Pangenome Graph for Chapter 5, titled "Pan-Genome Graph Alignment Improves Detection of Large INDELs in T-Cell Acute Lymphoblastic Leukaemia from mRNA Sequencing Data"
Scripts to Build the ALL Pangenome Graph and process sample data can be found at https://github.com/ashleethomson/ALL_GenomeGraph