Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data

Tiago F. Jesus*, Bruno Ribeiro-Gonçalves, Diogo N. Silva, Valeria Bortolaia, Mário Ramirez, João A Carriço

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

Plasmid ATLAS (pATLAS, http://www.patlas.site) provides an easy-to-use web accessible database with visual analytics tools to explore the relationships of plasmids available in NCBI's RefSeq database. pATLAS has two main goals: (i) to provide an easy way to search for plasmids deposited in NCBI RefSeq and their associated metadata; (ii) to visualize the relationships of plasmids in a graph, allowing the exploration of plasmid evolution. pATLAS allows searching by plasmid name, bacterial host taxa, antibiotic resistance and virulence genes, plasmid families, and by sequence length and similarity. pATLAS is also able to represent in the plasmid network, plasmid sets identified by external pipelines using mapping, mash screen or assembly from high-throughput sequencing data. By representing the identified hits within the network of relationships between plasmids, allowing the possibility of removing redundant results, and by taking advantage of the browsing capabilities of pATLAS, users can more easily interpret the pipelines' results. All these analyses can be saved to a JSON file for sharing and future re-evaluation. Furthermore, by offering a REST-API, the pATLAS database and network display are easily accessible by other interfaces or pipelines.
Original languageEnglish
JournalNucleic acids research
Volume47
Issue numberD1
Pages (from-to)188-194
ISSN0305-1048
DOIs
Publication statusPublished - 2019

Cite this

Jesus, T. F., Ribeiro-Gonçalves, B., Silva, D. N., Bortolaia, V., Ramirez, M., & Carriço, J. A. (2019). Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data. Nucleic acids research, 47(D1), 188-194. https://doi.org/10.1093/nar/gky1073
Jesus, Tiago F. ; Ribeiro-Gonçalves, Bruno ; Silva, Diogo N. ; Bortolaia, Valeria ; Ramirez, Mário ; Carriço, João A. / Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data. In: Nucleic acids research. 2019 ; Vol. 47, No. D1. pp. 188-194.
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abstract = "Plasmid ATLAS (pATLAS, http://www.patlas.site) provides an easy-to-use web accessible database with visual analytics tools to explore the relationships of plasmids available in NCBI's RefSeq database. pATLAS has two main goals: (i) to provide an easy way to search for plasmids deposited in NCBI RefSeq and their associated metadata; (ii) to visualize the relationships of plasmids in a graph, allowing the exploration of plasmid evolution. pATLAS allows searching by plasmid name, bacterial host taxa, antibiotic resistance and virulence genes, plasmid families, and by sequence length and similarity. pATLAS is also able to represent in the plasmid network, plasmid sets identified by external pipelines using mapping, mash screen or assembly from high-throughput sequencing data. By representing the identified hits within the network of relationships between plasmids, allowing the possibility of removing redundant results, and by taking advantage of the browsing capabilities of pATLAS, users can more easily interpret the pipelines' results. All these analyses can be saved to a JSON file for sharing and future re-evaluation. Furthermore, by offering a REST-API, the pATLAS database and network display are easily accessible by other interfaces or pipelines.",
author = "Jesus, {Tiago F.} and Bruno Ribeiro-Gon{\cc}alves and Silva, {Diogo N.} and Valeria Bortolaia and M{\'a}rio Ramirez and Carri{\cc}o, {Jo{\~a}o A}",
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Jesus, TF, Ribeiro-Gonçalves, B, Silva, DN, Bortolaia, V, Ramirez, M & Carriço, JA 2019, 'Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data', Nucleic acids research, vol. 47, no. D1, pp. 188-194. https://doi.org/10.1093/nar/gky1073

Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data. / Jesus, Tiago F.; Ribeiro-Gonçalves, Bruno; Silva, Diogo N.; Bortolaia, Valeria; Ramirez, Mário; Carriço, João A.

In: Nucleic acids research, Vol. 47, No. D1, 2019, p. 188-194.

Research output: Contribution to journalJournal articleResearchpeer-review

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AU - Jesus, Tiago F.

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AU - Ramirez, Mário

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