Citation¶

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

VNtyper 2¶

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 its 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 use 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 use 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