Dovetail Genomics Chicago® Promo
Improve Order, Orientation and Contiguity in your genome assemblies
Whether you have or are looking to create a de novo assembly or enhance an existing one (regardless of the techniques you have already used), we have the solutions to generate or improve your assembly, giving it order, orientation and contiguity up to full Chromosomes using our proprietary combination of Chicago® and Dovetail™ Hi-C.
In this example, the left panel shows that scaffolding with Chicago® in vitro proximity ligation data reduces the overall contiguity (scaffold N50) of the assembly from ~5.9 Mb to ~2.9 Mb as false mis-joins have been broken. Scaffolding with Dovetail™ Hi-C alone (right panel) dramatically improves contiguity to a scaffold N50 of 44.4Mb. Scaffolding with a combination of Chicago® and Dovetail™ Hi-C (centre panel) provides a similar level of N50 improvement, but a substantially better N90 improvement compared to Dovetail™ Hi-C alone. In addition, the Chicago® data corrects contig order and orientation errors, thereby producing a more accurate assembly.
With the fine scale information that Chicago® provides, Dovetail is able to identify mis-joins and improve the accuracy of contig order and orientation. The X axis is genomic location and the Y axis shows the size separation of read pair connections. The top version of the assembly is inaccurate – the red and blue contigs are oriented incorrectly, thus read pairs do not map and are displaced above in a distinctive pattern. The bottom assembly was corrected by HiRise™ using Chicago® scaffolds and now the read pairs align in the expected distances.
Long read technologies are a great starting point for challenging genomes. Unfortunately, they are often burdened by excessive repeat regions. If you are unable to link across those repeat regions, you will have an assembly with gaps or incorrect links between scaffolds. Chicago® in vitro proximity ligation gives linkage information across repeat regions and other regions that are traditionally hard to map, generally for regions that are 150kb or shorter. As you can see in this example, the combination of Chicago® with HiRise™ enabled identification of misjoins and then corrected these misjoins by making breaks and rejoining scaffolds in the correct order and orientation giving longer and more accurate contiguity. Then by adding in Dovetail™ Hi-C, you are able to achieve up to Chromosome scale assemblies.