Wastewater QC workflow in GalaxyTrakr (SSQuAWK4) v2

PURPOSE: Step-by-step instructions for checking sequence quality for SARS-CoV-2 wastewater samples using SSQuAWK: SARS - CoV - 2 Sequence Quality Assurance Workflow and Kontraption. The SSQuAWK 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 SSQuAWK workflow 5. Interpret the results Protocol and SSQuAWK workflow version history: Protocol V8 SSQuAWK version 4: Protocol version 8 has minor text corrections. The SSQuAWK version 4 workflow required minor edits on an updated backend system of GalaxyTrakr, and thus is now labeled as "SSQuAWK4.0.2" in GalaxyTrakr. All SSQuAWK4 protocol steps listed in this guide are applicable to SSQuAWK4.0.2. Protocol V7 SSQuAWK version 4: Protocol now includes a QC determination guidance table. The SSQuAWK version 4 workflow required minor bug edits on the backend, thus is now labeled as "SSQuAWK4.0.1" in GalaxyTrakr. All SSQuAWK4 protocol steps listed in this guide are applicable to SSQuAWK4.0.1. Protocol V6 SSQuAWK version 4: Best practice guidance on fastq.gz file uploads and new QC metric. Protocol V5 SSQuAWK version 3: Previous protocol version had broken links for FASTA and BED files, this version fixes the links. 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. Protocol V3, SSQuAWK version 2: Addition of 5 new genome mapping metrics Protocol V2, SSQuAWK version 1: Addition of a detailed 12 minute video tutorial Protocol V1, SSQuAWK version 1: Basic protocol steps with screenshots Participation was supported by the: Research Participation Program at the U.S. Food and Drug Administration administered by the Oak Ridge Institute for Science and Education (ORISE) through an interagency agreement between the U.S. Department of Energy and the U.S. Food and Drug Administration. Joint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland by the Food and Drug Administration (FDA) of the U.S. Department of Health and Human Services (HHS). The American Rescue Plan Act of 2021, Congress provided temporary funding for FDA to develop the capacity to sequence SARS-CoV-2 RNA from wastewater samples and to conduct a sampling and sequencing project through 2022.