Help Dovetail populate the Tree of Life!
We are pleased to announce the Dovetail Genome Assembly Award Program (DT-GAAPTM)
Apply now for the chance to receive matching funds up to $7,500*
At Dovetail Genomics, we build the most accurate and contiguous de novo assemblies available using our revolutionary combination of Chicago® in vitro proximity ligation and Dovetail™ Hi-C. We have assembled more than 800 genomes thus far and are excited to add even more to our Tree of Life with the Dovetail Genome Assembly Award Program. Whether you are in need of a full de novo assembly or are looking to improve an existing assembly, we have a solution for you.
The submission deadline is October 31st, 2018 @ 11:59 PM (ET) and award winners will be notified by email or phone no later than November 22nd, 2018.
*Please see DT-GAAP Terms and Conditions for full details.
Overview of the Dovetail De Novo Assembly Process
When building a de novo genome assembly for your favorite organism, assembly contiguity and accuracy are equally important. We are now accepting applications for the Dovetail Genome Assembly Award Program (DT-GAAP™). Let the de novo experts at Dovetail build you an accurate and contiguous genome assembly or improve an existing assembly with our two proprietary proximity ligation methods, Chicago® and Dovetail™ Hi-C, and our leading scaffolding software, HiRise™.
Our end-to-end service begins with a draft assembly of the genome. This can either be provided by you or built here at Dovetail using the right sequencing technology for your genome – we will consult with you to decide on the approach. Our minimum quality requirement at this stage is a scaffold N50 >20Kb.
We then use our proprietary Chicago® in vitro proximity ligation data to build up assembly contiguity by making long-range joins. Our scaffolding software, HiRise™, uses this data to find and correct false misjoins in the input assembly.
We then build Dovetail™ Hi-C libraries using intact cells or tissue. HiRise™ uses the Dovetail™ Hi-C data to make even longer range connections, up to full chromosomes, thereby greatly increasing contiguity.
The final assembly will be both highly contiguous (Chicago® + Dovetail™ Hi-C) and highly accurate (Chicago®). Our bioinformatics team will manually inspect the final assembly, ensuring the highest level of quality, before delivery.
Decode your organism with the DT-GAAPTM
Dovetail’s genome assembly services and products will take your research to the next level.
Correct Misjoins to Improve Contig Order and Orientation
In this example, a polyploid plant, an input scaffold N50 of 5.980Mb was lowered to 2.915Mb by Chicago® + HiRise™. When HiRise™ has high confidence a join has been made incorrectly in the input de novo assembly, it will break that join thereby improving overall accuracy.
Dovetail™ Hi-C data was applied to the interim Chicago® assembly and contiguity was dramatically improved, from an N50 of 2.915Mb to 44.288Mb. Thus, Chicago® and Dovetail™ Hi-C complement each other to provide a final assembly that is both accurate and contiguous.
Note that when Dovetail™ Hi-C alone is applied to the original input assembly, a comparable final scaffold N50 is reached (44.449Mb), but the scaffold N90 is significantly lower (19.818Mb vs. 26.550Mb).
Improve your organism’s assembly with the DT-GAAPTM
Chicago® data builds assembly contiguity by making long-range joins between distant contigs and scaffolds in the input assembly. With this bowfin* assembly, an input scaffold N50 of only 24Kb was boosted to over 10Mb with Chicago® plus HiRise™.
*acknowledgement to Ingo Braasch (Michigan State, project leader), Andrew W. Thompson (Michigan State), Solomon David (Nicholls State University), Allyse Ferrara (Nicholls State University), and the GenoFish Consortium for their work on this project.
Reduce Background Noise
In vivo Hi-C data contains noise from biological events, such as TADs, highlighted by red arrows (left), while Chicago® in vitro proximity ligation data is far cleaner (right). The Chicago® data therefore enables high resolution identification and correction of misjoins in the input assembly.
Unlike Hi-C libraries that are created in situ with natural chromatin, Chicago® libraries are built from high molecular weight DNA that is reconstituted into artificial chromatin. Artificial chromatin does not form looping structures, greatly improving signal to noise, and enabling high resolution detection of contig order and orientation errors.
In addition to contiguity improvement, Chicago® data serves another very important function. HiRise™ uses Chicago® data to find and correct contig order and orientation errors in the input assembly. High confidence misjoins are corrected by HiRise™, thereby improving the overall accuracy of the final assembly. In this example, a false join (circled) is clearly evident in the Chicago® plot, but not visible in the Hi-C plot. Hi-C data does not have the resolution to reveal contig order and orientation errors.
Grow the Tree of Life with the DT-GAAPTM
Chicago® Boosts Contiguity to Enable Hi-C
Hi-C requires an input scaffold N50 of ~1Mb to work effectively. In this example, weeping lovegrass, applying Hi-C directly to the low contiguity input assembly did not result in a chromosome-scale level of improvement (top table, 0.38Mb to 5.187Mb).
*acknowledgement to Mario Caccamo, José Carballo, Bruno Santos, Emidio Albertini and Vivianna Echenique for their work on this project.
However, when the Chicago® assembly was then scaffolded with DovetailTM Hi-C (lower table), a dramatic improvement in contiguity was seen (0.791Mb to 45.345Mb). Chicago® was needed to boost the assembly contiguity to a point where Dovetail™ Hi-C could then work effectively.
Get the most contiguous and accurate genome assembly with the DT-GAAPTM
Unlock your organism’s genome with the DT-GAAPTM