preprocessing and assembly workflows for Illumina data prepped following the COVIDSeq protocol


The COVIDSeqSEassembly.wdl workflow was developed for the preprocessing and assembly of Illumina COVIDSeq sequencing of SARS-CoV-2 to be run on the GCP Terra platform. It takes single-end short read fastq files as input.

The columns for the input data table in Terra should be arranged as:

  1. entity:sample_id (column of sample names/ids). If there is m

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