Running on HPC

Syndirella can be run easily via CLI on a HPC. While Syndirella itself does not have the capability to run in parallel on multiple threads, I’ve found running simultaneous jobs for each scaffold with low memory (3GB) to significantly increase speed.

Preparing the input files to run on HPC with example scripts for SLURM is found at syndirella/hpc.

Follow the example jupyter notebook to prepare everything, syndirella/hpc/prepare_csvs_jobs.ipynb.