uceasy 0.3.1

Wrapper for the Phyluce phylogenomics software package

UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs)

UCEasy is a Python wrapper that standardizes, automates, and simplifies the following PHYLUCE tasks: quality control of raw reads, assembly, alignment and UCE loci extraction.

Although the PHYLUCE pipeline is robust and well-established, it requires the execution of many command line scripts from heterogeneous tools, which can be quite challenging for scientists without some training in bioinformatics.

For more information check out our Wiki.

Installation Guide

Dependencies

• Python ^3.7
• PHYLUCE 1.6.* (1.7 not supported yet)

Install the package from PyPI:

$ pip install uceasy

Then, make sure you have a working installation of PHYLUCE, check out the installation guide at PHYLUCE's documentation.

Workflow

The operations Trim, Assemble and Align represent the following workflow. The following image demonstrates how the PHYLUCE workflow is abstracted by UCEasy.

The colored boxes are UCEasy CLI commands.

$ uceasy trim
$ uceasy assemble
$ uceasy align

Explore the options for these commands with the --help flag.

For a guide of how to use UCEasy see: Tutorial.

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)

Instituto Nacional de Pesquisas da Amazônia (INPA)

Centro Universitário do Estado do Pará (CESUPA)

Funding

This research was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq (fellowships 149985/2018-5; 129954/2018-7). Romina Batista was supported by a postdoctoral fellowship granted from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brasil (CAPES-INPA proc. 88887477562/2020-00).

Authors

Caio Vinícius Raposo Ribeiro
Lucas Peres Oliveira
Romina Batista
Marcos Paulo Alves de Sousa

Contact

Dr. Marcos Paulo Alves de Sousa (Project leader)

Email: [e-mail]
Laboratório de Biologia Molecular-LBM
Grupo de pesquisa em Bioinformática e Informática para Biodiversidade (BioInfo)
Museu Paraense Emílio Goeldi
Av. Perimetral 1901. CEP 66077- 530. Belém, Pará, Brazil.