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](

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