The folder denbi_gg contains the development space for Ansible playbooks and conda environment files. These are meant to be used to install graph genome software on virtual machines quickly.
Additionally, in the folder evaluation_pipeline there is a pipeline to assess the performance of three state-of-the-art genotyping algorithms (PanGenie, BayesTyper and GraphTyper). The pipeline uses genomes graphs provided by the "Human Genome Structural Variant Consortium" (HGSVC) and it is applied to a standard benchmarking sample NA24385/HG002 of the "Genome In A Bottle" (GIAB).
- ansible (in your local machine)
We tested the installation with ansible [core 2.14.3], however, other versions should work, as well.
The playbook was tested in deNBI (Deutsches Netzwerk für Bioinformatik-Infrastruktur) VMs with the following OS:
- Ubuntu 20.04
- Ubuntu 22.04
Funding provided by the BMBF - Förderkennzeichen 031L0184B.