Proksee

Proksee performs genome assembly, analysis, and graphical mapping of bacterial genomes from Illumina sequence reads or pre-assembled contigs to support genome characterization and comparative analyses.

Key Features:

• Data Input Flexibility: Accepts Illumina sequence reads in compressed FASTQ format, pre-assembled contigs in raw, FASTA, or GenBank formats, a GenBank accession number, or a Proksee map in JSON format.
• Assembly and Visualization: Performs genome assembly for raw sequence data and generates customizable graphical maps of bacterial genomes that can be used to launch additional analysis jobs.
• Unique Assembly Metrics: Provides assembly metrics via a custom reference database to evaluate assemblies against established benchmarks.
• Integrated Genome Browser: Includes an integrated genome browser for viewing and comparing analysis results at individual base resolution.
• Embedded Analysis Tools: Offers a suite of embedded analysis tools whose results can be incorporated into graphical maps or exported in alternative formats.
• Data Export Options: Enables export of graphical maps, analysis results, and log files.

Scientific Applications:

• Bacterial genome characterization: Facilitates characterization of bacterial genomes through assembly and integrated analyses.
• Genomic assembly benchmarking: Enables evaluation and benchmarking of genome assemblies against a custom reference database.
• Comparative genomics: Supports comparative analyses of bacterial genomes using graphical maps and an integrated genome browser.

Methodology:

Performs genome assembly for raw Illumina reads and operates on a multi-server cloud-based system designed to scale with user demand.