Benchmarking Parabrick's GPU-accelerated tools
Welcome to parabricks-benchmark! Before getting started, we highly recommend reading through parabricks-benchmark's documentation.
The ./parabricks-benchmark pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions:
parabricks-benchmark run: Run the parabricks-benchmark pipeline with your input files.parabricks-benchmark unlock: Unlocks a previous runs output directory.parabricks-benchmark install: Download reference files locally.parabricks-benchmark cache: Cache remote resources locally, coming soon!
parabricks-benchmark is pipeline to test and compare different GPU-accelerated parabricks tools against the tools they were inspired from. It relies on technologies like Singularity1 to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing steps orchestrated by Snakemake2, a flexible and scalable workflow management system, to submit jobs to a cluster.
The pipeline is compatible with data generated from Illumina short-read sequencing technologies. The GATK germline pipeline was tested using NIST's GIAB HG002, HG003, HG004 samples.
Before getting started, we highly recommend reading through the usage section of each available sub command.
For more information about issues or trouble-shooting a problem, please checkout our FAQ prior to opening an issue on Github.
Requires: singularity>=3.5 snakemake<8.0
The pipeline uses the offical parabricks docker image. With that being said, snakemake and singularity must be installed on the target system. Snakemake orchestrates the execution of each step in the pipeline. To guarantee the highest level of reproducibility, each step of the pipeline will rely on versioned images from DockerHub. Snakemake uses singularity to pull these images onto the local filesystem prior to job execution, and as so, snakemake and singularity will be the only two dependencies in the future.
Please clone this repository to your local filesystem using the following command:
# Clone Repository from Github
git clone https://github.com/OpenOmics/parabricks-benchmark.git
# Change your working directory
cd parabricks-benchmark/
# Add dependencies to $PATH
# Biowulf users should run
module load snakemake singularity
# Get usage information
./parabricks-benchmark -hThis site is a living document, created for and by members like you. parabricks-benchmark is maintained by the members of OpenOmics and is improved by continous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our GitHub repository.
If you use this software, please cite it as below:
@BibText
Citation coming soon!
@APA
Citation coming soon!
1. Kurtzer GM, Sochat V, Bauer MW (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE 12(5): e0177459.
2. Koster, J. and S. Rahmann (2018). "Snakemake-a scalable bioinformatics workflow engine." Bioinformatics 34(20): 3600.