Incidence of SARS-CoV-2 in SRA metagenomic samples

The Sequence Read Archive (SRA) is a repository of genomics data from the next generation of sequencing platforms. We would like to process all of the data deposited in the previous 6 months in the SRA to detect SARS-CoV-2. The ability to scan this archive will give us a better idea of the background levels of SARS-CoV-2 in metagenomics samples and will allow us to better track the temporal and spatial spread of the virus. We will download data from the SRA and use 4 different algorithms, GOTTCHA2, Centrifuge, Kraken2 and PanGIA to determine which sequences contain SARS-CoV-2