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).

Preprint

Please find our preprint here (opens in a new tab), which can be cited in the following way

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 (2024), doi.org/10.1016/j.ajhg.2024.06.007 (opens in a new tab)
• S. Schloissnig, S. Pani et al. Long-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project. bioRxiv (2024) 10.1101/2024.04.18.590093 (opens in a new tab)

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

See also

Additionally, you may be interested in these tools:

• Parascopy (opens in a new tab) for copy number analysis and variant calling within segmental duplications,
• Pileuppy (opens in a new tab): fast and colorful BAM/CRAM pileup,
• DuploMap (opens in a new tab) for improving long read alignments to segmental duplications.