Tag: phasing

New genome assembly method makes fruitful advances in genomic technology

Posted on April 29, 2021 by - Genomics, Hi-C, Proximo

 

A collaboration between Phase Genomics and Pacific Biosciences of California is bringing about the next generation of genome assembly technology. A newly published software tool, FALCON-Phase, combines genomic proximity ligation methods developed by Phase Genomics™, with the high accuracy, long-read sequencing data from PacBio®, enabling researchers to create haplotype-resolved genome sequences on a chromosomal scale, without having parental genome data. This method and its application to several animal genomes was published today in Nature Communications.

cow, zebra finch, and human hand arranged in a collage

Humans, as well as other animals, carry DNA sequence copies from both parents. These parental sequence “haplotypes” can carry millions of mutations unique to one of the parents and are often very relevant to diseases and other genetic traits. Until recently, accurately separating paternal and maternal mutations on the whole-genome scale required sequence information from the individual parents or extensive efforts that relied heavily on imputation from population studies. The new method employs the physical proximity information captured by proximity ligation (a technology also known as “Hi-C”) to separate maternal and paternal haplotype information from long-read genome assemblies. This development significantly increases the actionable information content coming out of genome sequencing studies.

 

 

“It’s an exciting time for genome assembly and PacBio HiFi sequencing continues to lead the way in this area with its powerful combination of read length and accuracy,” wrote Jonas Korlach, Chief Scientific Officer at Pacific Biosciences. “Phase Genomics Hi-C complements PacBio technology by extending our data into the ultra-long-range domain, enabling us to connect phase blocks and deliver chromosome-scale diploid assemblies without parental data. We are fortunate to have this excellent partnership with Phase Genomics, and we look forward to continuing to work together to create the highest quality reference genomes available.”

 

Assembling two fully-phased genomes in a single, streamlined process not only saves on the costs of research, but it also enables scientists to upgrade their genome assembly pipelines and obtain previously unobtainable information.

 

Dr. Erich Jarvis, professor at Rockefeller University and chair of the international Vertebrate Genomes Project, wrote, “Chromosome-scale haplotype phasing is critical for generating accurate genome assemblies and for understanding genomic variation within a species.” Furthermore, FALCON-Phase produces maternal and paternal haplotypes without family-trio data, so it can be applied to wild-caught samples or organisms lacking pedigree information. Jarvis notes, “In wild populations that many work with, parental samples are usually unavailable and therefore we need a method that can phase paternal and maternal sequences in the offspring individuals. With FALCON-Phase, we are able to use the Hi-C data that we have already generated for genome scaffolding and add a new dimension to every genome assembly, even retrospectively for previous projects. Our collaboration with Phase Genomics and PacBio has been extremely fruitful and the combination of the two technologies through FALCON-Phase will be highly beneficial to genomic sequencing efforts focused on conservation.”

 

FALCON-Phase is applicable to any diploid genome, including plants, animals, and fungi. It is available as free of charge open-source software (https://github.com/phasegenomics/FALCON-Phase) and Phase Genomics offers services that include the application of this method to varying genome projects. See the latest news and publications on this and other genome assembly methods at https://phasegenomics.com/resources-and-support/publications/.

 

For more information, email us at info@phasegenomics.com.

Phase Genomics Transformative Genome Phasing Tool (FALCON-Phase) Now Compatible with Nanopore Sequencing

Posted on October 28, 2019 by - Uncategorized

Nanopore and Hi-C produce a new fully-phased, chromosome-scale genome for the red raspberry.

On October 22, scientists at KeyGene revealed the first fully-phased, chromosome-scale reference genome for the red raspberry, sequenced with Oxford Nanopore long-read technology and scaffolded and phased into full chromosomes using Phase Genomics’ Proximo™ Hi-C method.  

Assembling complex plant genomes used to be considered nearly impossible as they can be extremely large, polypoid, and contain highly repetitive regions. Long-read sequencing generates genomic data spanning very long regions, but still needs to be scaffolded, or “put together” into chromosomes. Proximo Hi-C not only helps guide the assembly to produce chromosome-level scaffolds but can also tell which sequences and mutations come from the maternal and paternal chromosome copies (this is called phasing). Our phasing method, FALCON-Phase was originally released in 2018 and was used in conjunction with the Proximo pipeline to generate this “platinum level” raspberry genome.

Read more about the assembly and future directions for the project here.

Phase Genomics and Pacific Biosciences Co-Developing new Genome Assembly Phasing Software

Posted on April 19, 2018 by - Genomics, Proximo

Phase Genomics and Pacific Biosciences logos

“FALCON-Phase” – an algorithm for producing diploid genomes.

 

Phase Genomics has entered into a co-development agreement with Pacific Biosciences to develop FALCON-Phase, a software module that combines Hi-C and PacBio® highly-accurate, long read sequencing data to produce fully-phased diploid genome assemblies. The software will be released later this spring.

FALCON-Phase augments PacBio Single Molecule, Real-Time (SMRT®) assemblies with Hi-C proximity-ligation data, generating accurate, fully-phased diploid assemblies. Specifically, it uses Hi-C’s chromatin proximity information to identify sequences belonging to the same parental chromosome in genome assemblies produced by PacBio’s FALCON-Unzip software, greatly reducing haplotype switching along the primary assembly.

Furthermore, by combining Phase Genomics’ Proximo Hi-C genome scaffolding technology with FALCON-Phase, users can fully reconstruct maternal and paternal haplotypes on a chromosomal scale. The end result is a diploid set of chromosome-scale scaffolds, or two fully-phased genomes for the same data and labor cost typical for a single genome project.

FALCON-Phase genome Phasing Graph

FALCON-Phase groups long-read contigs into two separate haplotypes based on Hi-C data. Red and blue edges show contigs connected to the same haplotype, while black edges show homologous contigs connected to both haplotypes. Colors were assigned based on known phasing of assembly, which was not otherwise used to inform FALCON-Phase analysis.

These high-quality phased haplotypes can be leveraged to improve the efficiency of agricultural breeding programs, and could help identify disease-causing genomic variations in humans.

Prof. John Williams, Director of the Davies Research Centre at the University of Adelaide, Australia, wrote, “We are interested in expression of imprinted genes and for this work the availability of haplotype-resolved genome assemblies is an important advance. The release of software that enables the creation of haplotyped genome sequence assembly will revolutionize exploration of genome function. The FALCON-Phase software has this ability and can be applied retroactively to SMRT assemblies, as long as Hi-C data are available. Therefore, even pre-existing genomes can potentially be upgraded to haplotyped assemblies for little or no cost.”

Haplotype-resolved genome assembly is an exciting emerging field. Currently, there is only one other method, Trio Canu, which, unlike FALCON-Phase, requires the parents and offspring to be sequenced, adding an additional cost. For many species, it is not possible to collect a trio in the wild and breeding is often not an option. Other Hi-C phasing techniques exist, but they phase genetic variants, not genome assemblies.

The addition of ultra-long genomic interactions captured by Hi-C to PacBio assemblies is very powerful and presents a straightforward solution to a problem experienced by almost all genomic researchers working with diploid organisms.

A formal announcement with more information is coming in the next month. For more information, email us at info@phasegenomics.com.

 

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