riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions
The vast majority of bacterial genome sequencing has been performed using Illumina short reads. Because of the inherent difficulty of resolving repeated regions with short reads alone, only ~10 of sequencing projects have resulted in a closed genome. The most common repeated regions are those coding for ribosomal operons (rDNAs), which occur in a bacterial genome between 1 and 15 times and are typically used as sequence markers to classify and identify bacteria. Here, we show that the genomic context in which rDNAs occur is conserved across taxa and that, by utilizing the conserved nature of rDNAs across taxa and the uniqueness of their flanking regions, it is possible to improve assembly of these regions relative to de novo sequencing. We describe a method which constructs targeted pseudocontigs generated by iteratively assembling reads that map to a reference genome's rDNAs. These pseudocontigs are then used to more accurately assemble the newly-sequenced chromosome. We show that this method, implemented as riboSeed, correctly bridges across adjacent contigs in bacterial genome assembly and, when used in conjunction with other genome polishing tools, can assist in closure of a genome.
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