What is AdaOrder?

• An algorithm for tailoring the minimizer order to a particular dataset for improving the efficiency of binning applications.


• AdaOrder stands for Adaptive Order, as the algorithm is adapting the order iteratively to the dataset of interest.


• AdaOrder was developed by Dan Flomin, David Pellow, and Ron Shamir.

What is DGerbil?

• DGerbil is a k-mer counter based on the memory efficient k-mer counter Gerbil (https://github.com/uni-halle/gerbil). It integrates AdaOrder initialized with signature order and our bin mapping algorithm into Gerbil for improved efficiency.


• DGerbil was developed by Dan Flomin, David Pellow, and Ron Shamir.

Where is the paper and software for AdaOrder and DGerbil?

• AdaOrder is available on Github.


• DGerbil is available on Github.


• A preprint describing AdaOrder and DGerbil can be found on bioRxiv.


• It can be cited as follows:
  Flomin, D., et al "Dataset-adaptive minimizer order reduces memory usage in k-mer counting". bioRxiv (2021).

How can I get help?

• For questions or suggestions please contact Ron Shamir.