minisv | Qin AIM Lab

该项目发展长读长体细胞结构变异（SV）检测框架，结合 pangenome graphs 和 de novo personal genome assembly，相比仅依赖参考基因组的流程提高灵敏度和精确度 (Qin et al., 2025)。

肿瘤基因组在重复、高变异和低可比对区域中包含大量 SV，而这些区域常常导致参考基因组流程系统性漏检。通过组装每位个体的基因组，并在 pangenome-aware 坐标下比较肿瘤和匹配正常样本 reads，该方法能够恢复复杂体细胞事件，包括大型 indels、mobile element insertions 和 tandem duplications。源码见 GitHub。相关工作还包括基于 co-assembly graphs 的 long-range somatic SV caller colorSV (Le et al., 2025)，以及从长读长数据联合检测和定相 small、structural 和 mosaic variants 的 LongcallD (Gao et al., 2026)。

参考文献

2026

bioRxiv

LongcallD: joint calling and phasing of small, structural and mosaic variants from long reads

Yan Gao, Wen-Wei Liao, Qian Qin, and 2 more authors

bioRxiv, Mar 2026

DOI Bib HTML Code

@article{Gao2026LongcallD,
  title = {{LongcallD}: joint calling and phasing of small, structural and mosaic variants from long reads},
  author = {Gao, Yan and Liao, Wen-Wei and Qin, Qian and Hall, Ira M and Li, Heng},
  journal = {bioRxiv},
  pages = {2026.03.20.713111},
  month = mar,
  year = {2026},
  doi = {10.64898/2026.03.20.713111},
}

2025

bioRxiv

Improving long-read somatic structural variant calling with pangenome and de novo personal genome assembly

Qian Qin, Jakob Heinz, and Heng Li

bioRxiv, Oct 2025

DOI Bib HTML

@article{Qin2025LongReadSV,
  title = {Improving long-read somatic structural variant calling with pangenome and de novo personal genome assembly},
  author = {Qin, Qian and Heinz, Jakob and Li, Heng},
  journal = {bioRxiv},
  pages = {2025.10.28.685154},
  month = oct,
  year = {2025},
  doi = {10.1101/2025.10.28.685154},
}

GPB

colorSV: Long-range Somatic Structural Variation Calling from Matched Tumor-normal Co-assembly Graphs

M K Le, Qian Qin, and Heng Li

Genomics, Proteomics & Bioinformatics, Sep 2025

DOI Bib HTML Code

@article{Le2025colorSV,
  title = {{colorSV}: Long-range Somatic Structural Variation Calling from Matched Tumor-normal Co-assembly Graphs},
  author = {Le, M K and Qin, Qian and Li, Heng},
  journal = {Genomics, Proteomics \& Bioinformatics},
  pages = {qzaf082},
  month = sep,
  year = {2025},
  doi = {10.1093/gpbjnl/qzaf082},
}