Do you use genomes from NCBI and are concerned they may contain contaminant sequences? Now you can view reports generated for all prokaryotic and eukaryotic genomes with NCBI’s quality assurance tool, Foreign Contamination Screen (FCS), to better understand possible issues that may affect your studies.
What reports are available?
- Summary reports to select better assemblies at thresholds of your choosing.
- Detailed reports to remove or mask contaminant sequences so they don’t adversely affect analyses. This is particularly useful for building k-mer databases.
- Individual assembly reports available through the FTP link located on NCBI Datasets genome pages.
- Reports are available for all eukaryotic and prokaryotic GenBank and RefSeq assemblies, currently covering over 2.7 million assemblies.
- A README to understand how to interpret and use contamination reports.
Learn More
Want to run FCS on your own assembly? For more information about FCS and for step-by-step instructions on how to use it, check out our help documentation on GitHub.
Visit the contamination screening page to learn more about the screening process and how assemblies are marked as contaminated.
Read all about FCS in our recent publication in Genome Biology.
Stay up to date
FCS is part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.
Join our mailing list to keep up to date with FCS and other CGR news.
Questions?
We want to hear from you! 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 info@ncbi.nlm.nih.gov.