Metadata-Version: 2.1
Name: uceasy
Version: 0.2.0b1
Summary: Wrapper for the Phyluce phylogenomics software package
Home-page: https://uceasy.github.io
License: MIT
Keywords: uce,phyluce,ultraconserved elements
Author: Caio Raposo
Author-email: caioraposo@protonmail.com
Requires-Python: >=3.7,<4.0
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Dist: click (>=7.0,<8.0)
Project-URL: Repository, https://github.com/uceasy/uceasy
Description-Content-Type: text/markdown

<p>
    <img src="docs/img/uceasy_logo.jpg" height="200px">

</p>

[![Tests](https://github.com/uceasy/uceasy/workflows/Tests/badge.svg)](https://github.com/uceasy/uceasy/actions?workflow=Tests)
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# UCEasy: a wrapper for the Phyluce software package


__UCEasy__ is a wrapper to automate manual procedures of the [Phyluce](https://phyluce.readthedocs.io/en/latest) software package by abstracting the pipeline steps in only one command, easing the execution and improving reproducibility.


At the moment, the only software for _in silico_ analysis of [ultraconserved elements](https://www.ultraconserved.org/) (UCEs) is Phyluce, but its execution can be quite challenging especially for non-computer experts.
__UCEasy__ is a convenient tool that automates the execution of common tasks for all types of UCE analysis, these being [Quality Control](https://phyluce.readthedocs.io/en/latest/quality-control.html), [Assembly](https://phyluce.readthedocs.io/en/latest/assembly.html) and [UCE Processing](https://phyluce.readthedocs.io/en/latest/uce-processing.html).

## Pros
* Automation of the pipeline steps
* Easier to execute
* Extensible software architecture


## Installation Guide
### Dependencies
* Python ^3.7
* Python's official package installer (pip)
* Conda (for installing Phyluce)

## Acknowledgements

We thank the following institutions, which contributed to ensuring the success of our work:

Ministério da Ciência, Tecnologia, Inovação e Comunicação (MCTIC)

Museu Paraense Emílio Goeldi (MPEG)

Centro Universitário do Estado do Pará (CESUPA)

## Funding

This work has been supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq (grants 149985/2018-5; 129954/2018-7).

## Authors

 Marcos Paulo Alves de Sousa<br>
 Caio Vinícius Raposo Ribeiro <br>
 Lucas Peres Oliveira <br>
 Romina do Socorro da Silva Batista

 ## Contact

Dr. Marcos Paulo Alves de Sousa (Project leader)

_Email: **msousa@museu-goeldi.br**_<br>
_Laboratório de Biologia Molecular_<br>
_Museu Paraense Emílio Goeldi_<br>
_Av. Perimetral 1901. CEP 66077- 530. Belém, Pará, Brazil._

