NVIDIA Parabricks

• Parabricks offers range of accelerated NGS data processing tools/commands

• Parabricks documentation:

  “Parabricks was built from the ground up by GPU computing and Deep Learning experts who wanted to develop the fastest and most efficient possible implementation of common genomics algorithms.”

• We can use these commands and create a simple NGS data processing workflows with two main stages

  • Read mapping and alignment refinement

  • Variant calling

Ref:

Parabricks workflow (basic workflow)

Stage 1: Read mapping and alignment refinement

Step 1: fq2bam

Source

Step 2: applybqsr

• Compatible GATK4 Command: gatk ApplyBQSR

Stage 2: Variant calling

Parabricks HaplotypeCaller

Source