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OligoCounter and its related standalone visualisation programs are written in Java. The Java runtime environment version 1.5.0 (Java 5) or better is required. Java is available here.

Absolutely no warranty, implied or otherwise, is supplied with these programs. Use at your own risk! Although every effort has been made to check results are correct, they may still contain some bugs. Please notify the author of any bugs found.


Distribution with example


Programs are currently available as JAR files without the source code. We intend to release the full program and source code under the GPL following publication.

Please contact: davenport <dot> colin <at> mh-hannover.de

Helpful scripts

Some programs have been implemented in the programming language Python, available here. Otherwise we recommend the use of the linux programs such as "grep" for looking at this data in detail. 

The statistical language R is also very good with histograms for looking at positions of various oligos.