Overview:
- This pipeline can simulate a diploid individual with snps, indels and optinally structural variation on a reference genome of choice. Specify the individual in
config/config.yaml
. - Hifi + HiC reads can be simulated from this genome
- Hifiasm is run using the simulated reads
- Yahs and other tools can be run to scaffold the assembly graph created by Hifiasm
- The resulting assembly is evaluated by Quast
- Clone this repo.
- You unfortunately need to manually install pbsim3. This can be done by running
./install_pbsim.sh
. GFAse also needs to be installed manually (but this tool is not used by the main pipeline). - Install Python requirements:
pip install -r requirements.txt
- Test that the pipeline works:
snakemake --use-conda -F test_hifiasm
(should finish without errors in ~2 minutes)
See the rule test_quast
in rules/test.smk
.
snakemake --use-conda -F test_quast
- Genome simulation is hardcoded in config and the same for all simulations. Should be possible to configure for a given run
- Heterozygosity is fixed, should be tunable. Every variant is now default heterozygous.