Auger/Auspice/UShER: SARS-CoV-2 Cluster Detection Workflow for the Terra Platform v1

The Titan_Augur workflows was written to process concatenated assembly fasta data for SARS-CoV-2 Phylogenetics analysis and cluster detection. Augur has two workflows, Augur_Prep and Augur_Run which you need to run one after the other. The output of these workflows is the required inputs for Auspice/Nextstrain to understand the genetic relatedness and draw phylogenetics inferences. The inputs for the Augur_Prep job include metadata on the sample (you can upload as a tsv), the assembly fasta and pango lineage for each sample. If you ran Titan on Terra you will already have generate the the assembly fasta and pango lineage for samples, but if you used another pipeline you will need to upload them. Upon initiating a Augur_Prep job, input data will be processed and the output will be a sample metadata and assemblies in the correct format to perform Augur_run analysis. The Augur_run workflow then takes the metadata and the concatenated fasta assemblies to generate the outputs that can be used for phylogenetics inferences on Auspice or Nextstrain visualization interface tools. This protocol also shows steps on how to visualize using the Auspice as well as UCSC UShER tools. Here are some helpful viedos: Theiagen training video on Augur https://www.youtube.com/watch?v=r92L-B6wWOU https://www.youtube.com/watch?v=4nPS5Vab2dE https://www.youtube.com/watch?v=uDXBcHR8GSQ&t=2186s