Description of folders:
- centromere_annotation contains one liners and scripts to generate to:
- merge, colorize, manipulate repeat annotations
- extract, align, and analyze the putative centromere monomer sequence (monomer analysis)
- extract specific sequences and their protein counterparts, e.g. CENPA (protein finder)
- completeness contains one liners and scripts to annotate gaps in the previous reference relative to the T2T assembly
- coverage contains scripts to compute read coverage statistics
- figures contains scripts used to generate panels in the associated manuscript
- graph_annotation contains one liners and scripts to annotate the Verkko graph prior to assembly graph manual curation
- hpc_to_ref contains commands to generate alignments from homopolymer-compressed space to the lineare reference
- rDNA contains one liners and scripts to generate haplotype-specific rDNA models
- TEs contains one liners and scripts to annotate TEs
- verkko_consensus contains commands and scripts helpful when iteratively improving the consensus sequence towards T2T