This is a modified version of our COVIDSeqSEassembly workflow to handle shorter (35bp) reads:


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

This is a companion discussion topic for the original entry at