StrainSeeker is a program for detecting bacterial strains from raw sequencing reads. Compared to other similar programs, it offers the following advantages:

• Fully customizable database - use your own strains of interest or download our database
• Detect novel strains that are related to strains in the database
• Quickly handle large amounts of data
• Results given all the way down to the strain level!
• View publication online in PeerJ

StrainSeeker is meant to be used as a command line program but feel free to test it in a simple web interface for small samples.

If you have any questions, suggestions or problems with the program, please let us know.

Also, as we are constantly working to make StrainSeeker better, we are happy to analyze challenging datasets. If your research project involves bacterial community analysis and you need help in processing your data, contact us and we might be able to help you.