Proksee: in-depth characterization and visualization of bacterial genomes

Nucleic Acids Res. 2023 Jul 5;51(W1):W484-W492. doi: 10.1093/nar/gkad326.


Proksee ( 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Nucleic Acid
  • Genome, Bacterial*
  • Internet
  • Reproducibility of Results
  • Software*