Parabricks验证记录

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1.parabricks介绍
NVIDIAParabricks是一款可扩展的基因组学分析软件套件，利用全栈加速计算在几分钟内处理数据。它与所有领先的测序仪器兼容，支持不同的生物信息学工作流程，并集成了人工智能以实现准确性和定制。Parabricks是一种成本效益高、节省空间的解决方案，是专注于推进疾病理解和管理的大型基因组学项目的理想选择。

2.parabricks能做什么？
germline, somatic, and RNA analysis.
hc-solution-overview-parabricks-2756341.pdf

3.参考手册
https://docs.nvidia.com/clara/parabricks/4.0.0/index.html
parabricks包括哪些软件
Parabricks 4.0.0-1 has a significantly reduced set of tools. We are focusing primarily on the following tools:
applybqsr、bam2fq、bammetrics、bamsort、bqsr、collectmultiplemetrics、dbsnp
、deepvariant、deepvariant_germline、fq2bam、genotypegvcf、germline、haplotypecaller
、indexgvcf、mutectcaller、postpon、prepon、rna_fq2bam、somatic、starfusion

parabricks支持wdl 和nextflow

https://github.com/clara-parabricks-workflows

4.软件安装要求
Any NVIDIA GPU that supports CUDA architecture 60, 70, 75, or 80 and has at least 16GB of GPU RAM. Parabricks has been tested on the following NVIDIA GPUs:
V100 T4
A10, A30, A40, A100, A6000

System Requirements:
A 2 GPU server should have at least 100GB CPU RAM and at least 24 CPU threads.
A 4 GPU server should have at least 196GB CPU RAM and at least 32 CPU threads.
A 8 GPU server should have at least 392GB CPU RAM and at least 48 CPU threads.

The following are software requirements for running Clara Parabricks.
An NVIDIA driver greater than version 465.32.* .
Any Linux Operating System that supports nvidia-docker2 Docker version 20.10 (or higher)

以前 nvidia支持docker的方式是对docker进行替换现在统一使用nvidia-docker2
https://github.com/NVIDIA/nvidia-docker/issues/1268
What's the difference between the lastest nvidia-docker and nvidia container runtime？

使用如下操作 将parabricks添加到咱们自己的仓库 方便后续给客户安装
docker pull nvcr.io/nvidia/clara/clara-parabricks:4.0.0-1
docker tag nvcr.io/nvidia/clara/clara-parabricks:4.0.0-1 dockerhub.genostack.com:8090/nvidia/clara-parabricks:4.0.0-1
docker images
docker push dockerhub.genostack.com:8090/nvidia/clara-parabricks:4.0.0-1

使用下面的命令获取测试数据
$ wget -O parabricks_sample.tar.gz \
"https://s3.amazonaws.com/parabricks.sample/parabricks_sample.tar.gz"

docker run \
      --gpus all \
      --rm \
      --volume $(pwd):/workdir \
      --volume $(pwd):/outputdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.0.0-1 \
    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

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https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/containers/clara-parabricks/tags
镜像下载地址

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https://developer.nvidia.com/blog/search-posts/?q=parabricks&faceted_search_industry_str=Healthcare+%26+Life+Sciences
一些应用案例