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

Caio Ribeiro,Lucas Oliveira,Romina Batista,Marcos De Sousa

doi:10.3897/bdj.9.e78132

Abstract

BackgroundThe use of Ultraconserved Elements (UCEs) as genetic markers in phylogenomics has become popular and has provided promising results. Although UCE data can be easily obtained from targeted enriched sequencing, the protocol for in silico analysis of UCEs consist of the execution of heterogeneous and complex tools, a challenge for scientists without training in bioinformatics. Developing tools with the adoption of best practices in research software can lessen this problem by improving the execution of computational experiments, thus promoting better reproducibility.New informationWe present UCEasy, an easy-to-install and easy-to-use software package with a simple command line interface that facilitates the computational analysis of UCEs from sequencing samples, following the best practices of research software. UCEasy is a wrapper that standardises, automates and simplifies the quality control of raw reads, assembly and extraction and alignment of UCEs, generating at the end a data matrix with different levels of completeness that can be used to infer phylogenetic trees. We demonstrate the functionalities of UCEasy by reproducing the published results of phylogenomic studies of the bird genus Turdus (Aves) and of Adephaga families (Coleoptera) containing genomic datasets to efficiently extract UCEs.

Highlights

In the last decade, new genome-subsampling methods have been developed as a cheaper and simpler alternative to complete genome sequencing, enabling the scientific community to better understand the evolutionary inter-relationships of species (Davey et al 2011, Andermann et al 2020)
We present UCEasy, an easy-to-install and easy-to-use software package with a simple command line interface that facilitates the computational analysis of Ultraconserved Elements (UCEs) from sequencing samples, following the best practices of research software
We demonstrate the functionalities of UCEasy by reproducing the published results of phylogenomic studies of the bird genus Turdus (Aves) and of Adephaga families (Coleoptera) containing genomic datasets to efficiently extract UCEs

Summary

Background

The use of Ultraconserved Elements (UCEs) as genetic markers in phylogenomics has become popular and has provided promising results. UCE data can be obtained from targeted enriched sequencing, the protocol for in silico analysis of UCEs consist of the execution of heterogeneous and complex tools, a challenge for scientists without training in bioinformatics. Developing tools with the adoption of best practices in research software can lessen this problem by improving the execution of computational experiments, promoting better reproducibility. We present UCEasy, an easy-to-install and easy-to-use software package with a simple command line interface that facilitates the computational analysis of UCEs from. We demonstrate the functionalities of UCEasy by reproducing the published results of phylogenomic studies of the bird genus Turdus (Aves) and of Adephaga families (Coleoptera) containing genomic datasets to efficiently extract UCEs. Keywords phylogenomics, ultraconserved elements (UCEs), research software, reproducibility, bioinformatics

Introduction

The Abstract

Results and conclusion