#Introduction Here, we present the Chinese Pangenome Reference 2.0 (CPC.Ref2), a major expansion in scale, resolution, and functional depth. CPC.Ref2 comprises 948 haplotype-resolved, near-T2T genome assemblies generated from 474 individuals representing 60 ethnic groups across China. In addition to achieving unprecedented assembly continuity and accuracy at population scale, CPC.Ref2 integrates multiple layers of functional genomics data, including full-length transcriptomes, chromatin accessibility profiles, and DNA methylation maps, enabling systematic annotation of coding and non-coding elements. This framework allows us to characterize population-specific structural variation, dynamic gene copy events, regulatory diversity, archaic introgression, and signatures of natural selection with high precision.
Genome assembly (hifiasm), QC, and contig-to-chromosome anchoring with T2T assessment against CHM13.
Multi-caller SNV & SV detection from PacBio HiFi data:
| Tool | Purpose |
|---|---|
| deepvariant/ | Small variant calling + HiPhase phasing & haplotagging (hg38 + chm13) |
| cuteSV/ | SV detection on PacBio HiFi reads (hg38 + chm13) |
| pbsv/ | SV detection on PacBio HiFi reads (hg38 + chm13) |
| sniffles/ | Long-read SV detection (hg38 + chm13) |
| sawfish/ | CNV/SV discovery on PacBio HiFi reads with copy-number awareness (hg38 + chm13) |
| svimasm/ | Assembly-based SV calling (diploid + haploid, hg38 + chm13) |
| PAV/ | Assembly-based variant calling (hg38 + chm13) |
| SVPOP/ | Population-level SV merging |
Minigraph-Cactus pangenome graphs for CPC2 samples (234 and 477 sample panels) on CHM13 and GRCh38.
Gene copy-number variation analysis (presence / absence detection) across populations.
Expression (eQTL) and chromatin accessibility (caQTL) mapping by TensorQTL.
Correspondence and requests for materials should be addressed to S.X. (Email: xushua@fudan.edu.cn). For technical questions and bug reports, please contact S.L. (Email: songyangli22@m.fudan.edu.cn).