clara-parabricks

Summary

Software Description

From the developer’s website: Parabricks is a software suite for performing secondary analysis of next generation sequencing (NGS) DNA and RNA data. It delivers results at blazing fast speeds and low cost. Clara Parabricks can analyze 30x WGS (whole human genome) data in about 25 minutes, instead of 30 hours for other methods. Its output matches commonly used software, making it fairly simple to verify the accuracy of the output.

General Linux

Clara Parabricks is available at MSI via a singularity image ( see here for documentation on singularity at MSI ). It expects NVIDIA GPUs to be available when it runs, so you will want to make sure you are using it on one of MSI’s GPU partitions on Mangi or Agate ( see here for a listing of available partitions ). An example Parabricks command might look like the following. This example command is adapted from the Docker-based FQ2BAM tutorial provided by NVIDIA. You will need to have followed their instructions for downloading and extracting the data from the Getting the Sample Data step of their tutorial before running these commands.

module load singularity
singularity run --nv \
 -B $(pwd):/workdir \
 -B $(pwd):/outputdir \
 --pwd /workdir \
 /software/singularity-images/clara-parabricks/4.0.0-1.sif \
 pbrun fq2bam \
 --ref /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta \
 --in-fq /workdir/parabricks_sample/Data/sample_1.fq.gz /workdir/parabricks_sample/Data/sample_2.fq.gz \
 --out-bam /outputdir/fq2bam_output.bam

The options used above are:

--nv lets singularity detect and use the NVIDIA GPUs available on the current host

-B $(pwd):/input_data mounts your current working directory on MSI to the path /input_data inside the container

--pwd /workdir tells singularity to run commands using /workdir inside the container as the working directory

The rest of the command specifies the location of the singularity image on MSI storage, and the Parabricks pbrun command you want to run.