github.com/DNAstack/PacBio_CoSA/CoSA

Analysis of PacBio SARS-CoV-2 data using the CoSA pipeline

This repo provides a WDL wrapper for running PacBio’s CoSA pipeline. The CoSA pipeline produces an assembly, variants file, and lineage assignment using PacBio SARS-CoV-2 HiFi data. This pipeline uses DeepVariant for variant calling, but [other variant callers are available](https://github.com/PacificBiosciences/CoSA/wiki/Var


This is a companion discussion topic for the original entry at github.com/DNAstack/PacBio_CoSA/CoSA