UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs)
The 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 c...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Pensoft Publishers
2021-12-01
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| Series: | Biodiversity Data Journal |
| Subjects: | |
| Online Access: | https://bdj.pensoft.net/article/78132/download/pdf/ |
| _version_ | 1811275905322975232 |
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| author | Caio Ribeiro Lucas Oliveira Romina Batista Marcos De Sousa |
| author_facet | Caio Ribeiro Lucas Oliveira Romina Batista Marcos De Sousa |
| author_sort | Caio Ribeiro |
| collection | DOAJ |
| description | The 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.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 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. |
| first_indexed | 2024-04-12T23:47:10Z |
| format | Article |
| id | doaj.art-81d09487e0e34d12bfb2fd8f40a86907 |
| institution | Directory Open Access Journal |
| issn | 1314-2828 |
| language | English |
| last_indexed | 2024-04-12T23:47:10Z |
| publishDate | 2021-12-01 |
| publisher | Pensoft Publishers |
| record_format | Article |
| series | Biodiversity Data Journal |
| spelling | doaj.art-81d09487e0e34d12bfb2fd8f40a869072022-12-22T03:11:50ZengPensoft PublishersBiodiversity Data Journal1314-28282021-12-01911010.3897/BDJ.9.e7813278132UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs)Caio Ribeiro0Lucas Oliveira1Romina Batista2Marcos De Sousa3Coordenação de Ciência da Computação, Centro Universitário do Estado do Pará (CESUPA)Instituto de Computação, Universidade Estadual de Campinas (UNICAMP)Gothenburg Global Biodiversity CentreCoordenação de Ciência da Computação, Centro Universitário do Estado do Pará (CESUPA)The 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.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 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.https://bdj.pensoft.net/article/78132/download/pdf/phylogenomicsultraconserved elements (UCEs)res |
| spellingShingle | Caio Ribeiro Lucas Oliveira Romina Batista Marcos De Sousa UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs) Biodiversity Data Journal phylogenomics ultraconserved elements (UCEs) res |
| title | UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs) |
| title_full | UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs) |
| title_fullStr | UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs) |
| title_full_unstemmed | UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs) |
| title_short | UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs) |
| title_sort | uceasy a software package for automating and simplifying the analysis of ultraconserved elements uces |
| topic | phylogenomics ultraconserved elements (UCEs) res |
| url | https://bdj.pensoft.net/article/78132/download/pdf/ |
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