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 has corrected 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. Along 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 has been 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, Chicago®, with HiRise™, was able to identify misjoins, identify proper order and orientation and rejoin those scaffolds giving longer contiguity. Then add in Dovetail™ Hi-C to achieve up to Chromosome scale assemblies.