Wrapper for the Phyluce phylogenomics software package
Project description
UCEasy: a wrapper for the PHYLUCE software package
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.
Installation Guide
Dependencies
- Python ^3.7
- PHYLUCE ^1.6
See releases for pre-built binaries for Linux. Or install it 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 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
Caio Vinícius Raposo Ribeiro
Lucas Peres Oliveira
Romina do Socorro da Silva Batista
Contact
Dr. Marcos Paulo Alves de Sousa (Project leader)
Email: msousa@museu-goeldi.br
Laboratório de Biologia Molecular
Museu Paraense Emílio Goeldi
Av. Perimetral 1901. CEP 66077- 530. Belém, Pará, Brazil.
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