Proksee: in-depth characterization and visualization of bacterial genomes
| Autor: | Jason R Grant, Eric Enns, Eric Marinier, Arnab Mandal, Emily K Herman, Chih-yu Chen, Morag Graham, Gary Van Domselaar, Paul Stothard |
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| Rok vydání: | 2023 |
| Předmět: | |
| Zdroj: | Nucleic Acids Research. |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkad326 |
| Popis: | Proksee (https://proksee.ca) provides users with a powerful, easy-to-use, and feature-rich system for assembling, annotating, analysing, and visualizing bacterial genomes. Proksee accepts Illumina sequence reads as compressed FASTQ files or pre-assembled contigs in raw, FASTA, or GenBank format. Alternatively, users can supply a GenBank accession or a previously generated Proksee map in JSON format. Proksee then performs assembly (for raw sequence data), generates a graphical map, and provides an interface for customizing the map and launching further analysis jobs. Notable features of Proksee include unique and informative assembly metrics provided via a custom reference database of assemblies; a deeply integrated high-performance genome browser for viewing and comparing analysis results at individual base resolution (developed specifically for Proksee); an ever-growing list of embedded analysis tools whose results can be seamlessly added to the map or searched and explored in other formats; and the option to export graphical maps, analysis results, and log files for data sharing and research reproducibility. All these features are provided via a carefully designed multi-server cloud-based system that can easily scale to meet user demand and that ensures the web server is robust and responsive. |
| Databáze: | OpenAIRE |
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