Assessing sequence quality in GalaxyTrakr v2

EXTERNAL LINK https://galaxytrakr.org Assessing sequence quality in GalaxyTrakr V.1 Ruth Timme , Sai Laxmi Gubbala Venkata , Maria Balkey , Robyn Randolf , William Wolfgang , Errol Strain 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, Association of Public Health Laboratories, Silver Spring, Maryland, USA, Center for Veterinary Medicine, U.S. Food and Drug Administration, College Park, Maryland, USA Works for me dx.doi. org/10.17504/protocols.io. babuianw Ruth Timme US Food and Drug Administration Mar 17, 2020 1 2 3 4 2 5 1 2 3 4 5 GenomeTrakr Tech. support email: genomeTrakr@fda.hhs. gov 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 GalaxyTrakr 2. Create a new history/workspace 3. Upload data 4. Execute the MicroRunQC workflow 5. Interpret the results 1 1. Create a GalaxyTrakr account here: https://account.galaxytrakr.org/Account/Register 1.1 Log into your GalaxyTrakr account: https://galaxytrakr.org Account set up 1 1 03/17/2020 Cita tion : Ruth Timme, Sai Laxmi Gubbala Venkata, Maria Balkey, Robyn Randolf, William Wolfgang, Errol Strain (03/17/2020). Assessing sequence quality in GalaxyTrakr. https://dx.doi. org/10.17504/protocols.io. babuianw This is an open access protocol distributed under the terms of the Crea tive Com m ons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited 2 Create a new history. We recommend creating a new history for each new MiSeq Run and including the flow-cell ID and date in the history name. Save your MicroRunQC output here and any other relevant analyses, like serotyping, or AMR detection. After all the analysis output from this run is saved to your internal data network or computer, older history's should be purged/deleted so as not to occupy the limited storage space in your account. In some cases it may be useful to save, for a limited time, multiple histories or to run analyses concurrently in multiple histories. In these cases you need to pay attention to your % usage bar (shows % used of allocated storage space) in the upper right corner of the GalaxyTrakr page. If you need additional space you can contact galaxytrakrsupport@fda.hhs. gov and request additional storage. 2.1 Click on the + icon in the upper right History panel 2.2 Name your new History by clicking on the “Unnamed history”, type in desired name and hit enter. We recommend including the run cell ID and the date the run was started. 3 This section wi l l describe the process for uploading raw fastq fi les into your active History panel . After the files have been uploaded they will stay in your account until they are deleted. 3.1 Click on the upload/download icon on the top of the left web page to start an upload process. Create a new history