September 9, 2020  |  Data analysis

High Quality HiFi Assemblers Open Up a Wide New World of Genomics Possibilities

With PacBio HiFi sequencing data now readily available for organisms of any size, many exciting results have been published featuring new de novo assembly methods optimized for highly accurate long reads. These methods have produced assemblies for a variety of organisms at quality levels never before thought possible — as measured by completeness, contiguity and correctness. We feel privileged to collaborate with the scientific community on the development of these tools.
From Small to Tall
When the USDA wanted to rapidly assemble the Asian Giant Hornet as part of its real-time invasive species response initiative, they turned to a tool developed by our research and development team. Improved Phased Assembly (IPA), developed at PacBio by Ivan Sović  (@IvanSovic) and Zev Kronenberg (@zevkronenberg), is an assembler that delivers highly accurate, contiguous, and phased assemblies at very high speeds. 
Another new assembler called hifiasm proved useful when a PacBio team wanted to sequence the genome of the tallest living organism on earth: a California Coastal Redwood. PacBio’s own Greg Concepcion (@phototrophic) and colleagues were able to assemble a 48.5Gb redwood genome in just 6-days with 33-fold HiFi read coverage using the method, which was developed out of Heng Li’s (@lh3lh3) lab at Harvard. As described in this pre-print, co-authored by Concepcion, the method uses HiFi reads to produce haplotype-resolved de novo assembly with phased assembly graphs.  
Tackling the Tough Stuff

Visual representation of the most continuous HiFi-based assemblies of the CHM13 genome. Nurk, S et al. (2020) 

Not to be outdone, a new assembler from Sergey Koren (@sergekoren) and Adam Phillippy’s (@aphillippy) team at the National Human Genome Research Institute (NHGRI), HiCanu, demonstrates how it is now possible to sequence through even the most challenging regions of a human genome. PacBio’s own Rob Grothe is a co-author on the recently published work, which was also featured in a previous blog post.  
To hear more about the NHGRI’s work on Human Pangenome and Telomere-to-Telomere assemblies, check out the upcoming workshop on September 21-23, 2020: “T2T / HPRC Towards a Complete Reference of Human Genome Diversity.
Expanding What’s Possible
We are pleased by the possibilities of combining HiFi reads with these new rapid and high-quality genome assembly tools. Not only are they allowing us to tackle new organisms and reach new regions, they are enabling scientists to change the reference genome paradigm to create stand-alone de novo assemblies and pangenome collections with unparalleled speed and ease.   
To learn more, join us on September 16 for our webinar: Beyond a Single Reference Genome – The Advantages of Sequencing Multiple Individuals”. Or contact a PacBio Scientist to find out how HiFi reads can benefit your next research project.

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