Abstract
<p>PURPOSE: Step-by-step instructions for checking WGS sequence quality for bacterial pathogens. The MicroRunQC workflow, implemented in a custom Galaxy instance, will produce quality assessments for raw reads (Illumina paired-end fastq files) and draft de novo assemblies, along with reporting the sequence type for each isolate. This workflow will work on most microbial pathogens, so we advise laboratories to upload their entire MiSeq/NextSeq run through this workflow. SCOPE: This protocol covers the following tasks: 1. Quick access to GenomeTrakr sequence quality thresholds by organism 2. Create a GalaxyTrakr account 3. Set up an account in GalaxyTrakr 4. Create a new history/workspace 5. Upload data 6. Execute the MicroRunQC workflow 7. Interpret the results - check against GenomeTrakr QC thresholds Version updates: V10/11: Updating Cronobacter coverage threshold to 40X V9: Adding Aeromonas to QC thresholds V8: Updating screenshot for creating new history. V7: Edits to incorporate GalaxyTrakr upgrades and new interface. V6: Minor edits, including section reorganization and addition of clarifying notes V5: New column in the output table to capture additional mlst data fields when available in Sequence Type definition files (not available for all species) V4: MicroRunQC updated to V1.1 Includes updates to skeza and mlst methods, as well as adjusted assembly QC thresholds for E.coli. Added Enterobacter QC thresholds to threshold table. V3: updated with Cronobacter thresholds</p>