README.md

Compute4COVID

This is a getting started guide for using GPUs in Covid19/nCoV2019 genomic research.

We currently have the following guides:

1. Long Read Basecalling

Long Read Basecalling Guide

Using Bonito, a GPU-enabled basecaller, for SARS-CoV-2 DNA sequencing with Oxford Nanopore sequencing machines.

2. Short Read Alignment

Short Read Alignment Guide

Using the GPU-accelerated Parabricks BWA to align Illumina reads to a reference genome.

3. Long Read Polishing

Polishing Guide

Using Racon, a GPU accelerated polishing tool for long read based assemblies.