Merge branch 'main' of https://github.com/theLongLab/CATE into main

Author: DeshanPerera

README.md

@@ -5,13 +5,29 @@
 A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large-scale genomic data.
 
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+
+### Contents
+
+1️⃣ [Description](#description)  
+2️⃣ [News](#news)  
+3️⃣ [Prerequisites](#prerequisites)  
+4️⃣ [Installation Guide](#how-to-install)  
+5️⃣ [Running CATE](#how-to-run)    
+6️⃣ [Citations](#how-to-cite)  
+7️⃣ [Contact](#contact)  
+8️⃣ [License](#software-license)
+
+---
+
 #### Description
 
-The CATE software is a CUDA based solution to enable rapid processing of large-scale VCF files to conduct a series of six different tests on evolution.
+The CATE software is a CUDA-based solution to enable rapid processing of large-scale VCF files to conduct a series of six different tests on evolution.
 
-🔵 **Here we have provided only a brief overview of CATE's useability.**   
+🔵 **Here we have provided only a brief overview of CATE's usability.**   
 🟢 **Please refer to [CATE's wiki](https://github.com/theLongLab/CATE/wiki) to obtain a more detailed understanding of its functionality and usability.**
 
+[_Return to contents_](#contents)
+
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 #### News
@@ -21,10 +37,14 @@ The CATE software is a CUDA based solution to enable rapid processing of large-s
 Apollo is our high-performance viral epidemic simulation platform powered by CATE's architecture.
 
 Apollo is already available in CATE for use. Use the **--simulator** or **-sim** command. 
-Documentation on Apollo is available in our [wiki](https://github.com/theLongLab/CATE/wiki/Apollo), and a [user manual](https://github.com/theLongLab/CATE/tree/main/Apollo_User_Manual) has also been provided to get you up and running on our all-new tool.
+
+Documentation on Apollo is available in our [wiki](https://github.com/theLongLab/CATE/wiki/Apollo), and a [user manual](https://github.com/theLongLab/CATE/tree/main/Apollo_User_Manual) has also been provided. 
+Apollo also comes with a video tutorial. You can either download and watch it using the [GitHub repo tutorial](https://github.com/theLongLab/CATE/blob/main/Apollo_User_Manual/Apollo_video_tutorial.mp4) or watch it online via the [Vimeo link](https://vimeo.com/1079571253/571b3b6fd3). We hope these resources help you get up and running with our all-new tool.
 
 [Apollo's preprint is now available on bioRxiv](https://doi.org/10.1101/2024.10.07.617101).
 
+[_Return to contents_](#contents)
+
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 #### Prerequisites
 
@@ -33,6 +53,8 @@ Documentation on Apollo is available in our [wiki](https://github.com/theLongLab
 3. NVIDIA's CUDA toolkit (nvcc compiler)
 4. C++ compiler (gcc compiler)
 
+[_Return to contents_](#contents)
+
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 #### How to INSTALL
@@ -85,6 +107,9 @@ To ensure successful installation try running the following:
 ````
 CATE -h
 ````
+
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+
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 #### How to RUN
@@ -132,6 +157,8 @@ The __HELP__ menu will list all available functions and how each function can be
 
 > ./Test_Main -h
 
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 #### How to Cite
 
@@ -160,7 +187,9 @@ bioRxiv 2024.10.07.617101; [doi: https://doi.org/10.1101/2024.10.07.617101](http
 
 To cite CATE's code with Apollo's integration please cite the Zenodo release:
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13917864.svg)](https://doi.org/10.5281/zenodo.13917864)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15299962.svg)](https://doi.org/10.5281/zenodo.15299962)
+
+[_Return to contents_](#contents)
 
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 #### Contact
@@ -173,14 +202,16 @@ Dr. **Quan** Long (quan.long@ucalgary.ca)
 
 Dr. **Christian** D. Huber (cdh5313@psu.edu)
 
-2. For **Apollo** please address your correspondence to:
+2. For **Apollo**, please address your correspondence to:
 
 Dr. **Deshan** Perera (duwagedahampriyabala@ucalgary.ca)
 
 Dr. **Quan** Long (quan.long@ucalgary.ca)
 
 Dr. **Alexander** Platt (alexander.platt@pennmedicine.upenn.edu)
 
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+
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 #### Software License
 
@@ -206,4 +237,6 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
 
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+
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