# clara-parabricks

## Summary

+ **Support Level:** Secondary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [https://docs.nvidia.com/clara/parabricks/4.0.0/index.html](https://docs.nvidia.com/clara/parabricks/4.0.0/index.html)

## 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](https://www.msi.umn.edu/support/faq/how-do-i-use-singularity-centos-7)
). 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](https://www.msi.umn.edu/partitions) ). An example Parabricks
command might look like the following. This example command is adapted
from the [Docker-based FQ2BAM tutorial provided by
NVIDIA.](https://docs.nvidia.com/clara/parabricks/4.0.0/Tutorials/FQ2BAM_Tutorial.html#fq2bam-tutorial)
You will need to have followed their instructions for downloading and
extracting the data from the [Getting the Sample Data step of their
tutorial](https://docs.nvidia.com/clara/parabricks/4.0.0/Tutorials/GettingTheSampleData.html)
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.