Reference Graph Pangenome Data Analysis Hackathon 2023

Material for the Reference Graph Pangenome Data Analysis Hackathon 2023, November 13-17 in Cape Town, South Africa. The event was sponsored by H3ABioNet.

Table of Contents

• Reference-based pangenome graph building
  • Constructing and viewing your first graphs
• Small pangenome graph building from sequence alignments
  • Building HLA pangenome graphs
  • Building LPA pangenome graphs
• Human pangenome graph building from sequence alignments
  • Pangenome Sequence Naming
  • Sequence partitioning
  • Building chromosome-specific pangenome graphs
• Understanding pangenome graphs
  • MHC locus
  • Graph extraction
  • Graph untangling
  • Annotation injection
• Short read mapping and variant calling
• Hacking with our data