SD-COVID-Sequencing

My scripts/notes from the San Diego COVID sequencing effort. To see the general deployment of the pipeline created from these notes, see ViReflow:

https://github.com/niemasd/ViReflow

To see the expanded instantiation of the pipeline actually being used in production throughout San Diego County, see C-VIEW:

https://github.com/ucsd-ccbb/C-VIEW