GTO: A toolkit to unify pipelines in genomic and proteomic research
Next-generation sequencing triggered the production of a massive volume of publicly available data and the development of new specialised tools. These tools are dispersed over different frameworks, making the management and analyses of the data a challenging task. Additionally, new targeted tools ar...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2020-07-01
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| Series: | SoftwareX |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352711020301473 |
| _version_ | 1818393835991990272 |
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| author | João R. Almeida Armando J. Pinho José L. Oliveira Olga Fajarda Diogo Pratas |
| author_facet | João R. Almeida Armando J. Pinho José L. Oliveira Olga Fajarda Diogo Pratas |
| author_sort | João R. Almeida |
| collection | DOAJ |
| description | Next-generation sequencing triggered the production of a massive volume of publicly available data and the development of new specialised tools. These tools are dispersed over different frameworks, making the management and analyses of the data a challenging task. Additionally, new targeted tools are needed, given the dynamics and specificities of the field. We present GTO, a comprehensive toolkit designed to unify pipelines in genomic and proteomic research, which combines specialised tools for analysis, simulation, compression, development, visualisation, and transformation of the data. This toolkit combines novel tools with a modular architecture, being an excellent platform for experimental scientists, as well as a useful resource for teaching bioinformatics enquiry to students in life sciences. GTO is implemented in C language and is available, under the MIT license, at https://bioinformatics.ua.pt/gto. |
| first_indexed | 2024-12-14T05:51:38Z |
| format | Article |
| id | doaj.art-0e0cf3628ade4db2b651460067238538 |
| institution | Directory Open Access Journal |
| issn | 2352-7110 |
| language | English |
| last_indexed | 2024-12-14T05:51:38Z |
| publishDate | 2020-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | SoftwareX |
| spelling | doaj.art-0e0cf3628ade4db2b6514600672385382022-12-21T23:14:42ZengElsevierSoftwareX2352-71102020-07-0112100535GTO: A toolkit to unify pipelines in genomic and proteomic researchJoão R. Almeida0Armando J. Pinho1José L. Oliveira2Olga Fajarda3Diogo Pratas4Department of Electronics, Telecommunications and Informatics (DETI/IEETA), University of Aveiro, Aveiro, Portugal; Department of Information and Communications Technologies, University of A Coruña, A Coruña, Spain; Corresponding author at: Department of Electronics, Telecommunications and Informatics (DETI/IEETA), University of Aveiro, Aveiro, Portugal.Department of Electronics, Telecommunications and Informatics (DETI/IEETA), University of Aveiro, Aveiro, PortugalDepartment of Electronics, Telecommunications and Informatics (DETI/IEETA), University of Aveiro, Aveiro, PortugalDepartment of Electronics, Telecommunications and Informatics (DETI/IEETA), University of Aveiro, Aveiro, PortugalDepartment of Electronics, Telecommunications and Informatics (DETI/IEETA), University of Aveiro, Aveiro, Portugal; Department of Virology, University of Helsinki, Helsinki, FinlandNext-generation sequencing triggered the production of a massive volume of publicly available data and the development of new specialised tools. These tools are dispersed over different frameworks, making the management and analyses of the data a challenging task. Additionally, new targeted tools are needed, given the dynamics and specificities of the field. We present GTO, a comprehensive toolkit designed to unify pipelines in genomic and proteomic research, which combines specialised tools for analysis, simulation, compression, development, visualisation, and transformation of the data. This toolkit combines novel tools with a modular architecture, being an excellent platform for experimental scientists, as well as a useful resource for teaching bioinformatics enquiry to students in life sciences. GTO is implemented in C language and is available, under the MIT license, at https://bioinformatics.ua.pt/gto.http://www.sciencedirect.com/science/article/pii/S2352711020301473Genomic ToolkitProteomic ToolkitNext-generation sequencing |
| spellingShingle | João R. Almeida Armando J. Pinho José L. Oliveira Olga Fajarda Diogo Pratas GTO: A toolkit to unify pipelines in genomic and proteomic research SoftwareX Genomic Toolkit Proteomic Toolkit Next-generation sequencing |
| title | GTO: A toolkit to unify pipelines in genomic and proteomic research |
| title_full | GTO: A toolkit to unify pipelines in genomic and proteomic research |
| title_fullStr | GTO: A toolkit to unify pipelines in genomic and proteomic research |
| title_full_unstemmed | GTO: A toolkit to unify pipelines in genomic and proteomic research |
| title_short | GTO: A toolkit to unify pipelines in genomic and proteomic research |
| title_sort | gto a toolkit to unify pipelines in genomic and proteomic research |
| topic | Genomic Toolkit Proteomic Toolkit Next-generation sequencing |
| url | http://www.sciencedirect.com/science/article/pii/S2352711020301473 |
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