Quality control assessment for microbial genomes: GalaxyTrakr MicroRunQC workflow v3

PURPOSE: Step-by-step instructions for checking WGS sequence quality. 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. set up an account in GalaxyTrakr 2. Create a new history/workspace 3. Upload data 4. Execute the MicroRunQC workflow 5. Interpret the results V3: updated with Cronobacter thresholds