New Improvements! Try out our Foreign Contamination Screen (FCS) Tool

New Improvements! Try out our Foreign Contamination Screen (FCS) Tool

Want to submit high-quality data quickly and easily to GenBank? Check out our Foreign Contamination Screen (FCS) tool, a quality assurance process that you can run yourself. FCS offers enhanced contaminant detection sensitivity to improve your genome assemblies and facilitate high-quality data submissions to GenBank. We recently made several improvements to make the tool even easier to use! 

What’s New?
  • Now quicker and easier to run!  
  • Decontaminate your genome with just one extra step. 
    • Save the removed sequences in a separate file, if desired.  
  • More accurate!  
  • Find more contaminants with improved coverage of prokaryotes, protists, and more. 
  • Screen your genome on the cloud in minutes. 

See our release notes for technical details.  

Learn More

Learn how to use FCS, available from GitHub. For more information about FCS and for step-by-step instructions on how to use it, check out our help documentation.   

Stay up to date

FCS is part of the NIH Comparative Genomics Resource (CGR), an NLM project to establish an ecosystem to facilitate reliable comparative genomics analyses for all eukaryotic organisms. Join our mailing list to keep up to date with FCS and other CGR news.   


We want to hear from you! Try it out and let us know what you think. We are making ongoing improvements based on your feedback. If you have questions or would like to provide feedback, please reach out to us at 

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