Asian elephant VGP genome (mEleMax1)

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Pipeline for running the VGP assembly pipeline 2.0+

🚧 Under construction! 🚧

Requirements:

• Slurm
• Conda

Installation:

git clone https://github.com/diegomics/VGP_Asian_elephant
cd VGP_Asian_elephant

Hifiasm

purge_dups workflow

bionano worflow 🚧

Arima_mapping workflow

The Arima workflow uses up to 24 CPUs and 192 GB in certain steps

. bash install_arima_dependencies.sh

. Edit the file arima.cnf with required data

. Run the workflow with bash run_arima_pipeline.sh

*) For the Asian elephant genome, it takes <30 h to produce the final sorted BAM (needed for pretextMap) and ~44 h to produce the final sorted BED (needed for salsa2 or yahs). Comment the code for steps 13 and 14 in run_arima_pipeline.sh if BED files are not needed.

Salsa2 workflow