short_read_alignment

GPU-accelerated short read alignment using Parabricks

Parabricks provides GPU-accelerated BWA for short-read alignment to a reference genome.

Data

data/MN908947/MN908947.fasta is the reference genome for SARS-CoV-2 in FASTA format.

Installation

Follow the installation guide at https://www.nvidia.com/en-us/docs/parabricks/local-installation/

Run GPU-accelerated BWA

Once Parabricks is installed, the following command performs:

1. GPU-accelerated BWA-MEM
2. Co-ordinate sorting
3. Marking duplicates.

pbrun fq2bam --ref data/MN908947/MN908947.fasta --in-fq sample_1.fastq.gz sample_2.fastq.gz --out-bam output.bam