K12 assembly

Example syntenic dotplot comparison of a de novo assembled E. coli genome (x-axis) to a complete reference genome (y-axis)

Cheap sequencing brings cheap genomes! However, depending on the technology used to sequencing a genome, you will find that even with 50-100x sequencing coverage, a genome cannot be completely assembled. Due to repeat regions in the genome that are larger than the reads generated by the sequencing technology, pieces of the genome cannot be ordered relative to one another unless bac-ends are used to anchor these pieces relative to one another. What can CoGe do to help?

Fortunately, when it comes to many microbial genomes, there are already many complete genomes that can be used as a reference. SynMap is the perfect tool for comparing genomes.