diff --git a/README.md b/README.md index 3ceb54e8..4d26ecb3 100755 --- a/README.md +++ b/README.md @@ -2,11 +2,11 @@ [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](LICENSE) [![CI](https://github.com/smortezah/smashpp/actions/workflows/ci.yml/badge.svg)](https://github.com/smortezah/smashpp/actions/workflows/ci.yml) -A fast tool to find and visualize rearrangements in DNA sequences. +Smash++ is a fast utility designed for the identification and visualization of rearrangements in DNA sequences. ## Installation -Installing Smash++ requires CMake >=3.5 and a C++14 compliant compiler. +To install Smash++, you'll need CMake version 3.5 or higher, along with a compiler that supports C++14. ### Docker @@ -20,7 +20,7 @@ docker run -it smortezah/smashpp ### Conda -Install [Miniconda](https://docs.conda.io/en/latest/miniconda.html), then run the following: +Begin by installing [Miniconda](https://docs.conda.io/en/latest/miniconda.html). Once installed, execute the following commands: ```bash conda install -c bioconda -y smashpp @@ -53,7 +53,7 @@ bash install.sh ### Windows -Install [WSL](https://docs.microsoft.com/en-us/windows/wsl/install-win10) (Windows Subsystem for Linux), then clone Smash++ and install it, like in Ubuntu: +First, set up [WSL](https://docs.microsoft.com/en-us/windows/wsl/install-win10) (Windows Subsystem for Linux). After that, clone the Smash++ repository and proceed with the installation as you would on Ubuntu: ```bash git clone --depth 1 https://github.com/smortezah/smashpp.git; @@ -61,7 +61,8 @@ cd smashpp; ./install.sh ``` -**Note**: in all operating systems, in the case of permission denial, you can use the `sudo` command. +>[!NOTE] +> If you encounter permission issues on any operating system, consider using the `sudo` command. ## Usage @@ -69,23 +70,23 @@ cd smashpp; ./smashpp [OPTIONS] -r -t ``` -For example, +For example: ```bash ./smashpp -r ref -t tar ``` -It is recommended to choose short names for reference and target sequences. +For optimal results, it's advisable to select short names for both reference and target sequences. ### Options -To see the possible options for Smash++, type: +To explore the available options for Smash++, execute the following command: ```bash ./smashpp ``` -which provides the following: +which will yield the following: ```text SYNOPSIS @@ -200,7 +201,7 @@ OPTIONS show version ``` -To see the options for Smash++ Visualizer, type: +To explore the options available for the Smash++ Visualizer, enter the following command: ```bash ./smashpp viz @@ -212,7 +213,7 @@ or ./smashpp -viz ``` -which provides the following: +which will yield the following: ```text SYNOPSIS @@ -305,21 +306,21 @@ OPTIONS ### Example -After installing Smash++, copy its executable file into `example` directory and go to that directory: +Once Smash++ is installed, copy its executable file into the `example` directory and navigate to that directory: ```bash cp smashpp example/; cd example/ ``` -In this directory, there are two 1000 base sequences, the reference sequence named `ref`, and the target sequence named `tar`. Now, run Smash++ and the visualizer: +This directory contains two sequences, each 1000 bases long: the reference sequence (`ref`) and the target sequence (`tar`). To run Smash++ and the visualizer, use the following commands: ```bash ./smashpp -r ref -t tar; ./smashpp viz -o example.svg ref.tar.pos ``` -**Update**: since version 22.08, the JSON format is supported. To use it, run: +**Update**: As of version 22.08, Smash++ now supports the JSON format. To utilize this feature, execute the following command: ```bash ./smashpp --reference ref --target tar --format json; @@ -328,7 +329,7 @@ In this directory, there are two 1000 base sequences, the reference sequence nam ## Cite -Please cite the following, if you use Smash++: +If you find Smash++ useful in your research, please acknowledge our work by citing the following: * M. Hosseini, D. Pratas, B. Morgenstern, A.J. Pinho, "Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements," *GigaScience*, vol. 9, no. 5, 2020. [DOI: 10.1093/gigascience/giaa048](https://doi.org/10.1093/gigascience/giaa048) @@ -338,10 +339,10 @@ Please cite the following, if you use Smash++: ## Issues -Please let us know if there is any [issues](https://github.com/smortezah/smashpp/issues). +Should you encounter any [issues](https://github.com/smortezah/smashpp/issues), please don't hesitate to let us know. ## License -Copyright © 2018-2023 Morteza Hosseini. +Smash++ is protected under the [GNU GPL v3](http://www.gnu.org/licenses/gpl-3.0.html) license. -Smash++ is licensed under [GNU GPL v3](http://www.gnu.org/licenses/gpl-3.0.html). +Copyright © 2018-2024 Morteza Hosseini. \ No newline at end of file