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update readme #5

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danflomin Nov 30, 2021
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danflomin Nov 30, 2021
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14 changes: 9 additions & 5 deletions README.md
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# AdaOrder
AdaOrder is an algorithm for adapting the minimizer order to an input dataset.
It aims to flatten the k-mer load distribution across minimizers.

This implementation of AdaOrder corresponds to the following paper: .
This implementation of AdaOrder is described in 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`.

## Usage

Expand All @@ -29,6 +27,12 @@ AdaOrder can be controlled by several command line options and flags.
| `‑p <float>` | Set the penalty factor of AdaOrder. | `0.01` |
| `‑in <path>` | Dataset to generate AdaOrder for. | |


Precomputed orders: Orders computed by AdaOrder, on 4 datasets from the paper (H. Sapiens, A. Thaliana and fresh water metagenome) with `k=28,55`. By using them for other datasets from the same species, AdaOrder computing time can be drastically reduced or avoided altogether.




## DGerbil
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.