github.com/CDPHE/COVIDSeqSEassembly

COVIDSeqSEassembly:

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

COVIDSeqSEassembly.wdl

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

This is a companion discussion topic for the original entry at github.com/CDPHE/COVIDSeqSEassembly