Jorg

Jorg circularizes microbial genomes assembled from metagenomic datasets to confirm genome completeness and enable genomic-context and metabolic-inference studies.

Key Features:

• Circular Genome Assembly: Facilitates circularization of microbial genomes to confirm completeness and integrity, provide scaffolds for future assemblies, recover complete gene content, minimize contamination, study synteny, and link protein-coding genes with ribosomal RNA genes.
• Iterative Methodology: Employs an iterative approach combining assembly, binning, and read mapping to improve circularization accuracy and to identify potential misassemblies arising from k-mer-based assemblies.
• Focus on Candidate Phyla Radiation (CPR) and other small genomes: Applied to small genomes with single ribosomal RNA operons, including successful circularization of 34 CPR genomes and additional genomes from Margulisbacteria, Chloroflexi, and megaphages.
• Exposure of Novel Insights: Enables detection of genomic features such as non-operonic ribosomal genes in most CPR species and diverged forms of RNase P RNA.

Scientific Applications:

• Reference Collection Building: Produces circularized genomes that can be used to build reference collections serving as scaffolds for future genomic assemblies.
• Genomic Context Studies: Enables analysis of synteny and gene organization within complete circular genomes.
• Metabolic Inference Linkage: Allows linking of protein-coding genes to ribosomal RNA genes to support metabolic inference based on 16S rRNA gene sequencing.

Methodology:

Uses a semi-automated, iterative process of assembly, binning, and read mapping that identifies potential k-mer-derived misassemblies and is effective for small genomes with a single ribosomal RNA operon.