olekto / hic-assembly-benchmarking Goto Github PK

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

1. Clone this repo.
2. 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).
3. Install Python requirements: pip install -r requirements.txt
4. 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.