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.
In this repo we have both a version of cosigt running with snakemake and a shell workflow as a test. Cosigt has been packaged in guix and can be deployed as a docker or singularity container using the guix definition.
Install guix according to:
=> https://issues.genenetwork.org/topics/deploy/installation
You should be able to install cosigt with
unset GUIX_PROFILE # on Debian
mkdir ~/opt
source ~/opt/guix-pull/etc/profile
guix build cosigt
guix install cosigt -p ~/opt/cosigt
Next run cosigt with
unset GUIX_PROFILE # on Debian
source ~/opt/cosigt/etc/profile
cosigt -h
You can run the tests from this source tree with
cd cosigt/test
bash run_test.sh
./run_test_snakemake.sh
Troubleshooting: Note that if Guix starts building loads of stuff (particularly GO itself) you may need to configure guix substitutes.
=> https://issues.genenetwork.org/topics/deploy/installation
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