This zip file contains three workflows for CLC Genomics Workbench that are designed to work with QIAGEN's QIAseq SARSCOV2 amplicon sequencing panel. The zip archive will be automatically unzipped and the workflows can be open, edited, run directly, or installed for other users on the same system. zip archives provides above and import them into CLC Genomics Workbench using the Import->Standard Import option on the tool bar. Please contact me via email ( or Twitter ( if there's any major issue with any of these pipelines that need to be fixed. To the best of my ability, I have created these workflows to take into account aspects of the wet-lab protocols (where ever possible), and may include specific primer sequences, adapter sequences, or other parameter settings to account for differences in sequencing platforms(i.e. Each workflow includes - a minimum - qc, trim, mapping, variant calling and the output of a consensus sequence. The zip archives available here are intended to provide CLC Genomics Workbench users with a quick way to get started with analysis of SARS-CoV-2 genomics data from a variety of upstream laboratory protocols. CLC Genomics Workbench Workflows for SARS-CoV-2 Background QIAGEN kit handbooks and user manuals are available at ( or can be requested from QIAGEN Technical Services or your local distributor. For up-to-date licensing information and product-specific disclaimers, see the respective QIAGEN kit handbook or user manual. These products are not intended for the diagnosis, prevention or treatment of a disease. **ĭISCLAIMER QIAGEN Digital Insights provided here are intended for molecular biology applications only. If you have any questions - please DM me on Twitter or here on GitHub. They are intended as examples in the hopes that users may find them useful to get started quickly on analyzing their SARS-CoV-2 genomics data with CLC. ** The workflows found here are provided AS IS by Jonathan Jacobs, and not officially by QIAGEN Digital Insights. Please visit our COVID-19 Emergency Response Licenses page to request your licenses and access additional resources. Have fun!Īlso, free Extended Trials of both CLC Genomics ProSuite and Ingenuity Pathway Analysis are available from QIAGEN Digital Insights until June 15th, 2020. There you will find some downloadable workflows that can be imported, edited, and run in CLC.
If you are looking for some example workflows for using CLC with SARSCOV2 data - look under the "CLC-SARSCOV2-Workflows" folder. An unofficial repo for CLC Genomics Workflows, custom datasets, tutorials, and other files.
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