This repository contains results and code pertaining to the GenVarLoader manuscript. The GenVarLoader package itself is available from PyPI.
Publically available GVL datasets from the 1000 Genomes Project are available from Zenodo. All other data from the paper are controlled access.
To run benchmarks for the 1000 Genomes Project, download the tar archvies from Zenodo and extract them into ./throughput/datasets/1kgp. Then, some manual editing of the SLURM commands in ./throughput/launch_benchmarks.py may be required depending on whether SLURM is available and/or node names. In addition, the reference genome used by the 1000 Genomes Project should be downloaded to ./throughput/ from their FTP site.