From 6d4656f783b323a09e9ec6a5fcd28e4991c1cdb7 Mon Sep 17 00:00:00 2001 From: danflomin <33806717+danflomin@users.noreply.github.com> Date: Tue, 30 Nov 2021 20:40:23 +0200 Subject: [PATCH 1/2] update readme --- README.md | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 3a11365..799049c 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,9 @@ # 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 @@ -29,6 +27,11 @@ AdaOrder can be controlled by several command line options and flags. | `‑p ` | Set the penalty factor of AdaOrder. | `0.01` | | `‑in ` | Dataset to generate AdaOrder for. | | + +In `orders_minimizer_7.zip` are pre computed orders by AdaOrder, on 4 datasets used in the paper with `k=28,55`. + + + ## 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. From d3fdaf3311a1ffc53e86d7503b9bd9bd58d55f68 Mon Sep 17 00:00:00 2001 From: danflomin <33806717+danflomin@users.noreply.github.com> Date: Tue, 30 Nov 2021 20:54:04 +0200 Subject: [PATCH 2/2] update readme --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 799049c..f5f9bff 100644 --- a/README.md +++ b/README.md @@ -28,7 +28,8 @@ AdaOrder can be controlled by several command line options and flags. | `‑in ` | Dataset to generate AdaOrder for. | | -In `orders_minimizer_7.zip` are pre computed orders by AdaOrder, on 4 datasets used in the paper with `k=28,55`. +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. +