Citation¶

If you use VNtyper 2 in your research, please cite the following publications.

VNtyper 2 and VNtyper-Online (Preprint)¶

Popp B, Saei H, Teltsh O, Janoušek V, Přistoupilová A, Vrbacká A, Hartmannová H, Kidd K, Helmuth J, Bleyer AJ, Wiesener M, Fausch K, Rowan C, El Hassan E, Clince M, Cavalleri G, Locher M, Eckardt KU, Richter-Pechanska P, ADTKD-Net Consortium, Kmoch S, Antignac C, Conlon P, Dorval G, Živná M. VNtyper 2 enables open-access short-read genotyping of MUC1 VNTR variants in ADTKD at high-speed. medRxiv. 2026. doi:10.64898/2026.05.27.26352937

BibTeX¶

@article{popp2026vntyper2,
  title={VNtyper 2 enables open-access short-read genotyping of MUC1 VNTR variants in ADTKD at high-speed},
  author={Popp, Bernt and Saei, Hassan and Teltsh, Omri and Janou{\v{s}}ek, V{\'a}clav and P{\v{r}}istoupilov{\'a}, Anna and Vrback{\'a}, Alena and Hartmannov{\'a}, Hana and Kidd, Kendrah and Helmuth, Johannes and Bleyer, Anthony J and Wiesener, Michael and Fausch, Kathrin and Rowan, Colm and El Hassan, Elhussein and Clince, Michelle and Cavalleri, Gianpiero and Locher, Maurus and Eckardt, Kai-Uwe and Richter-Pechanska, Paulina and {ADTKD-Net Consortium} and Kmoch, Stanislav and Antignac, Corinne and Conlon, Peter and Dorval, Guillaume and {\v{Z}}ivn{\'a}, Martina},
  journal={medRxiv},
  pages={2026.05.27.26352937},
  year={2026},
  publisher={Cold Spring Harbor Laboratory Press},
  doi={10.64898/2026.05.27.26352937}
}

VNtyper v1 (Original Method)¶

Saei H, Moriniere V, Heidet L, et al. VNtyper enables accurate alignment-free genotyping of MUC1 coding VNTR using short-read sequencing data. iScience. 2023;26(7):107171. doi:10.1016/j.isci.2023.107171

BibTeX¶

@article{saei2023vntyper,
  title={VNtyper enables accurate alignment-free genotyping of MUC1 coding VNTR using short-read sequencing data},
  author={Saei, Hassan and others},
  journal={iScience},
  volume={26},
  number={7},
  pages={107171},
  year={2023},
  publisher={Elsevier},
  doi={10.1016/j.isci.2023.107171}
}

Kestrel¶

VNtyper 2 relies on the Kestrel variant caller for mapping-free k-mer-based genotyping. If you use VNtyper 2, please also cite the Kestrel publication:

Audano PA, Ravishankar S, Vannberg FO. Mapping-free variant calling using haplotype reconstruction from k-mer frequencies. Bioinformatics. 2018;34(10):1659-1665. doi:10.1093/bioinformatics/btx753

BibTeX¶

@article{audano2018kestrel,
  title={Mapping-free variant calling using haplotype reconstruction from k-mer frequencies},
  author={Audano, Peter A and Ravishankar, Shashidhar and Vannberg, Fredrik O},
  journal={Bioinformatics},
  volume={34},
  number={10},
  pages={1659-1665},
  year={2018},
  publisher={Oxford University Press},
  doi={10.1093/bioinformatics/btx753}
}

adVNTR (Optional Module)¶

If you enable the adVNTR module, please also cite:

Park J, Bakhtiari M, Popp B, et al. Detecting tandem repeat variants in coding regions using code-adVNTR. iScience. 2022;25(8):104785. doi:10.1016/j.isci.2022.104785

SHARK (Optional Module)¶

The SHARK module in VNtyper 2 is a re-implementation of the SHARK concept. If you enable it, please cite the original method:

Denti L, Pirola Y, Monti M, et al. SHARK: Fishing relevant reads in an RNA-Seq sample. Bioinformatics. 2021;37(4):464-472. doi:10.1093/bioinformatics/btaa779