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
2018 Nucleic Acids Research  
Plasmid ATLAS (pATLAS, provides an easy-to-use web accessible database with visual analytics tools to explore the relationships of plasmids available in NCBI's RefSeq database. pAT-LAS 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
more » ... xa, 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 reevaluation. Furthermore, by offering a REST-API, the pATLAS database and network display are easily accessible by other interfaces or pipelines.
doi:10.1093/nar/gky1073 pmid:30395323 fatcat:p4ctsykmd5e6ppsreh6aaj5r64