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URL: https://dx.doi.org/DOI:10.17504/protocols.io.bdvfi63n

Authors: Ruth Timme, Sai Laxmi Gubbala Venkata, Maria Balkey, Robyn Randolph, William Wolfgang, Errol Strain

Group: GenomeTrakr

Summary: PURPOSE: Step-by-step instructions for checking WGS sequence quality. The MicroRunQC workflow, implimented 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 isoalte. 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 GalaxyTrakr2. Create a new history/workspace3. Upload data4. Execute the MicroRunQC workflow5. Interpret the results

Affiliations: US Food and Drug Administration, Bacteriology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, USA, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA, Center for Veterinary Medicine, U.S. Food and Drug Administration, College Park, Maryland, USA, Wadsworth Center NYSDOH, Center for Veterinary Medicine, U.S. Food and Drug Administration, College Park, Maryland, USA

External URL: https://galaxytrakr.org

Version: 2

Publication Date: 2020

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