Wastewater QC workflow in GalaxyTrakr (SSQuAWK3) v4

PURPOSE: Step-by-step instructions for checking sequence quality for SARS-CoV-2 wastewater samples using SSQuAWK3: SARS - CoV - 2 Sequence Quality Assurance Workflow and Kontraption, version 3. The SSQuAWK3 workflow, implemented in CFSAN's custom Galaxy instance (GalaxyTrakr) will produce quality assessments for raw reads (Illumina MiSeq paired-end fastq files). SCOPE: This protocol covers the following tasks: 1. Set up an account in GalaxyTrakr 2. Create a new history 3. Upload data and reference files 4. Execute the SSQuAWK3 workflow 5. Interpret the results Protocol and SSQuAWK workflow version history: Protocol V1, SSQuAWK version 1: Basic protocol steps with screenshots Protocol V2, SSQuAWK version 1: Addition of a detailed 12 minute video tutorial Protocol V3, SSQuAWK version 2: Addition of 5 new genome mapping metrics Protocol V4 SSQuAWK version 3: Metrics now reported with fewer softwares, fewer underlying GalaxyTrakr jobs,and about 50% fewerunderlying GalaxyTrakr steps. Cleaner output table formats now include QC placeholder columns for SRA metadata template.