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Wrapper for the Phyluce phylogenomics software package

Project description

Tests Quality Gate Status DOI

UCEasy: a software package based on good practices in scientific computing for phylogenetic analysis of UCEs

UCEasy is a wrapper to automate manual procedures of the PHYLUCE software package by abstracting the pipeline steps into 3 major commands and choosing sensible defaults for its command-line options, easing the execution and improving reproducibility.

At the moment, the only software package for analysing ultraconserved elements (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 most types of UCE analysis, these being Quality Control, Assembly and UCE Processing.

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 Quality Control, Assembly and Phylogenomics represent the following workflow.

The colored boxes are UCEasy CLI commands.

$ uceasy quality-control
$ uceasy assembly
$ uceasy phylogenomics

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).

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: msousa@museu-goeldi.br
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.

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