Tutorials

Step-by-Step Tutorials

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These tutorials walk you through a simple use case for NVIDIA Parabricks, giving a brief introduction to how it works. We’ll start by downloading some sample data:

  • A reference file (Homo_sapiens_assembly38.fasta) and its index
  • A ‘known indels’ file and its index
  • Two FASTQ files
  • Associated index files
  • One BAM file for markdup
  • One single-ended BAM file

The tutorials then walk through the following steps:

  • Alignment (FASTA + FASTQ ==> BAM)
  • Variant calling (FASTA + BAM ==> VCF)

These tutorials are meant to be simple and straightforward and to only cover a single, specific use case. You should be able to copy and paste the commands into a terminal window and get the same results as shown. The Detailed Tutorials for Parabricks Pipelines cover more general problem solving using Parabricks.

Steps in the Tutorial