Hi Everyone, I'm interested in estimating DUF1220/Olduvai domain copy numbers (in NBPF genes on chr1q21.1) using the new high-coverage (~24–30x) Denisova 25 genome from Peyrégne et al. (2025 bioRxiv preprint: "A high-coverage genome from a 200,000-year-old Denisovan"). The improved structural variant calling in repetitive regions should enable more accurate counts than previous archaic assemblies. Prior Sikela lab work reported ~350 copies in Neanderthals (vs. ~270–320 in modern humans). Has anyone accessed the Denisova 25 data yet (promised deposition in ENA/GenBank; possibly early release on Max Planck EVA FTP like prior Denisovans) and run DUF1220 estimates?

If not, guidance on methods would be great:

Download chromosome 1 alignments/assembly. Use probe-based counting (e.g., Sikela lab scripts if public?). Alternatives: NCBI BLAST with known DUF1220 sequences, Tandem Repeats Finder, or CNV tools like cn.MOPS/Control-FREEC in R/Colab.

Any quick runs, tutorials, or pointers appreciated. I can give background on the importance of this request if needed, my email is needininfo@gmail.com Thanks!