This implementation of AdaOrder corresponds to the following paper: .
To cite this paper use the following form:
In orders_minimizer_7.zip are pre computed orders by AdaOrder, on 4 datasets used in the paper with k=28,55.
First, compile the source code using your compiler to "AdaOrder.jar".
AdaOrder generates 2 files in the working directory: freq.txt, ranks.txt.
ranks.txt is the file with the generated minimizer order [Algorithm 1 in our paper].
freq.txt is the file with the estimated sizes if minimizers bins [Algorithm 2 in our paper].
In both files: line i corresponds to the minimizer with value i using Natural, and its value is its (rank \ bin size) among all m-mers.
java -classpath "AdaOrder.jar" dumbo.OrderingOptimizer -in <input-file> <parameters>;
AdaOrder can be controlled by several command line options and flags.
| Option | Description | Default |
|---|---|---|
‑k <int> |
Set the length of k-mers. | 60 |
‑m <int> |
Set the length m of minimizers. | 7 |
‑R <int> |
Set the number of AdaOrder runs. | 1000 |
‑N <int> |
Set the number of samples per round of AdaOrder. | 100000 |
‑p <float> |
Set the penalty factor of AdaOrder. | 0.01 |
‑in <path> |
Dataset to generate AdaOrder for. |
DGerbil is a modification of Gerbil, a memory efficient k-mer counter, that uses AdaOrder instaed of signature, for improved memory usage. Its source code is found at https://github.com/Shamir-Lab/DGerbil.