Locityper

Locityper is targeted genotyper for complex polymorphic genes based on short and long-read whole genome sequencing. Locityper is created by Timofey Prodanov (opens in a new tab) timofey.prodanov[at]hhu.de and Tobias Marschall (opens in a new tab) tobias.marschall[at]hhu.de at the Marschall Lab (opens in a new tab), Heinrich Heine University Düsseldorf (opens in a new tab).

Locityper repository can be found here (opens in a new tab). Please, check if you are using the latest Locityper release (opens in a new tab).

Citation

Please check out our paper here (opens in a new tab).

T. Prodanov, E.G. Plender, G. Seebohm, S.G. Meuth, E.E. Eichler, T. Marschall. Locityper enables targeted genotyping of complex polymorphic genes. Nature Genetics (2025), doi.org/10.1038/s41588-025-02362-4 (opens in a new tab).

Installation

The easiest way to install Locityper is with conda (opens in a new tab). For that, please enable bioconda (opens in a new tab) channel, and run the following line:

conda install -c bioconda locityper

Installation should finish faster with mamba (opens in a new tab) utility (mamba install locityper).

Extended installation instructions can be found here, including instructions for the container platforms singularity (opens in a new tab) and docker (opens in a new tab).

Test dataset

You can find test dataset and corresponding instructions here.

Available data

Locityper genotype predictions and preprocessed data for the 1KGP samples can be found here.

Locityper applications

Locityper is actively applied in various research settings. You can find examples in the following manuscripts:

E. Plender et al. Structural and genetic diversity in the secreted mucins, MUC5AC and MUC5B. The American Journal of Human Genetics 111, 1700–1716 (2024), doi.org/10.1016/j.ajhg.2024.06.007 (opens in a new tab)
G. Logsdon et al. Complex genetic variation in nearly complete human genomes. Nature 644 430–441 (2025), doi.org/10.1038/s41586-025-09140-6 (opens in a new tab)
S. Schloissnig, S. Pani et al. Structural variation in 1,019 diverse humans based on long-read sequencing. Nature 644, 442–452 (2025), doi.org/10.1038/s41586-025-09290-7 (opens in a new tab)
W. Ma & M. Chaisson. Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes. Nature Genetics (2025), doi.org/10.1038/s41588-025-02346-4 (opens in a new tab)
K. Garimella et al. Population-scale Long-read Sequencing in the All of Us Research Program. medRxiv (2025), doi.org/10.1101/2025.10.02.25336942 (opens in a new tab)

Please, write me (timofey.prodanov[at]hhu.de) if you want to add your paper to this list.