riboSeed

riboSeed resolves repeated ribosomal DNA (rDNA) operons to improve prokaryotic genome assembly and facilitate genome closure, addressing regions that are difficult to resolve with short-read sequencing technologies such as Illumina.

Key Features:

• Targeted Subassembly Approach: Employs a targeted subassembly strategy focused on resolving gaps caused by repeated rDNA operons, which can range from 1 to 15 copies per bacterial genome.
• Pseudocontig Construction: Constructs pseudocontigs by iteratively assembling reads that map to reference genome rDNAs using conserved rDNA sequences and unique flanking regions within the genome.
• Improved Assembly Accuracy: Uses generated pseudocontigs to bridge adjacent contigs in bacterial genome assemblies, improving accuracy relative to de novo short-read assembly alone.
• Integration with Genome Polishing Tools: Integrates with genome polishing tools to aid closure of bacterial genomes by resolving repeated rDNA regions, a major barrier to achieving closed genomes (only ~10% of projects reach closure in some contexts).

Scientific Applications:

• Genome Assembly and Closure: Facilitates completion of bacterial genome assemblies by resolving gaps associated with rDNA operons.
• Bacterial Classification and Identification: Improves assembly of rDNA regions that serve as sequence markers for bacterial taxonomic classification and identification.

Methodology:

Leverages the genomic context of rDNA operons by exploiting conserved rDNA sequences across taxa and unique flanking regions within a genome; iteratively assembles reads mapped to reference genome rDNAs to produce pseudocontigs, which are then used to refine and bridge gaps between contigs.