<h3 align="center">Eukfinder</h3>
<p align="center">
project_description
<br />
<a href="https://github.com/dzhao2019/Share/wiki"><strong>Explore the docs »</strong></a>
<br />
<br />
<a href="https://github.com/dzhao2019/Share/wiki">View Demo</a>
·
<a href="https://github.com/dzhao2019/Share/wiki">Report Bug</a>
·
<a href="https://github.com/dzhao2019/Share/wiki">Request Feature</a>
</p>
</div>
<!-- TABLE OF CONTENTS -->
<details>
<summary>Table of Contents</summary>
<ol>
<li>
<a href="#about-the-project">About The Project</a>
<ul>
<li><a href="#built-with">Built With</a></li>
</ul>
</li>
<li>
<a href="#getting-started">Getting Started</a>
<ul>
<li><a href="#prerequisites">Prerequisites</a></li>
<li><a href="#installation">Installation</a></li>
</ul>
</li>
<li><a href="#usage">Usage</a></li>
<li><a href="#roadmap">Roadmap</a></li>
<li><a href="#contributing">Contributing</a></li>
<li><a href="#license">License</a></li>
<li><a href="#contact">Contact</a></li>
<li><a href="#acknowledgments">Acknowledgments</a></li>
</ol>
</details>
<!-- ABOUT THE PROJECT -->
## About The Project
<!-- GETTING STARTED -->
## Getting Started
This is an example of how you may give instructions on setting up your project locally.
To get a local copy up and running follow these simple example steps.
### Prerequisites
This is an example of how to list things you need to use the software and how to install them.
* npm
```sh
npm install npm@latest -g
```
### Installation
<p align="right">(<a href="#readme-top">back to top</a>)</p>
<!-- USAGE EXAMPLES -->
## Usage
**Eukfinder read_prep**
usage: Eukfinder read_prep [-h] --r1 R1 --r2 R2 -n THREADS -i ILLUMINA_CLIP
--hcrop HCROP -l LEADING_TRIM -t TRAIL_TRIM --wsize
WSIZE --qscore QSCORE --mlen MLEN --hg HG -o
OUT_NAME --cdb CDB
optional arguments:
-h, --help show this help message and exit
Required arguments:
Description
--r1 R1, --reads-r1 R1 left reads
--r2 R2, --reads-r2 R2 right reads
-n THREADS, --threads THREADS number of threads
-i ILLUMINA_CLIP, --illumina-clip ILLUMINA_CLIP adaptor file
--hcrop HCROP, --head-crop HCROP head trim
-l LEADING_TRIM, --leading-trim LEADING_TRIM leading trim
-t TRAIL_TRIM, --trail-trim TRAIL_TRIM trail trim
--wsize WSIZE, --window-size WSIZE sliding window size
--qscore QSCORE, --quality-score QSCORE quality score for trimming
--mlen MLEN, --min-length MLEN minimum length
--hg HG, --host-genome HG host genome to get map out
-o OUT_NAME, --out_name OUT_NAME out name
--cdb CDB, --centrifuge-database CDB path to centrifuge database
<!-- ROADMAP -->
## Roadmap
<p align="right">(<a href="#readme-top">back to top</a>)</p>
<!-- CONTRIBUTING -->
## Contributing
Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are **greatly appreciated**.
If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement".
Don't forget to give the project a star! Thanks again!
<p align="right">(<a href="#readme-top">back to top</a>)</p>
<!-- LICENSE -->
## License
Distributed under the MIT License. See `LICENSE.txt` for more information.
<p align="right">(<a href="#readme-top">back to top</a>)</p>
<!-- CONTACT -->
## Contact
<!-- ACKNOWLEDGMENTS -->
## Acknowledgments
<p align="right">(<a href="#readme-top">back to top</a>)</p>