Cosigt (COsine SImilarity-based GenoTyper) is a snakemake pipeline capable to assign structural haplotypes (that is, a genotype) to sequenced samples using pangenome graphs. An explanation of the rationale behind cosigt was first presented in this manuscript [2]. A detailed description of the pipeline and the algorithm is available in this preprint [1].
Extensive documentation describing how to set-up and run cosigt ia availbale in the online documentation.
This project is licensed under the MIT License - see the LICENSE file for details.
If you use cosigt in your research, please cite the following references:
[1] Bolognini, D. et al., (2026). Population-scalable genotyping from low-coverage sequencing data using pangenome graphs. bioRxiv 2026.02.05.704023
[2] Bolognini, D. et al., (2024). Recurrent evolution and selection shape structural diversity at the amylase locus. Nature 634, 617–625