SARS-CoV-2 pipeline live on EIT Pathogena
clinical microbiology
Back in the SARS-CoV-2 pandemic we worked closely with ORACLE Corp to build and deploy a bioinformatics pipeline in ORACLE Cloud that processes raw genetic files and infers what the consensus genome is and hence what lineage (e.g. BA.2) it belongs to. The heart of the pipeline is an amplicon-aware variant caller, viridian, that was written by Zamin Iqbal's group and there is a nice preprint out showing how it avoids various calling artefacts that can complicate phylogenetic tree construction.
An improved version of the pipeline has now been deployed, tested and launched on EIT Pathogena, a cloud-based genetics platform. Anyone can sign up and process at least 1,000 samples for free.