New open-source algorithm produces phased diploid genome assemblies

Seattle-based Phase Genomics [www.phasegenomics.com], the leader in Hi-C based genomic solutions and Pacific Biosciences of California, Inc. [www.pacb.com], the leader in long-read sequencing, announce the release of the FALCON-Phase software as part of a new co-development effort to improve the FALCON-Unzip genome assembly method for providing high-quality, phased diploid genome assemblies.

FALCON-Phase augments PacBio® Single Molecule, Real-Time (SMRT®) Sequencing-based assemblies with Hi-C proximity-ligation data to generate accurate phased diploid assemblies. Using Phase Genomics’ genome scaffolding technologies and FALCON-Phase, maternal and paternal haplotypes can be separated or “phased” on a chromosomal scale.

“You essentially get two genomes for the price of one with the FALCON-Phase software yielding both maternal and paternal haplotypes,” said Dr. Ivan Liachko, CEO and Co-founder of Phase Genomics, “The combination of SMRT Sequencing and long-range genomic contiguity captured by Hi-C data is very powerful and presents a straightforward solution to a problem experienced by almost all genomic researchers working with diploid organisms.”

High-quality phased haplotypes provided by FALCON-Phase can, among many other use cases, facilitate the study of inherited disease and be leveraged to improve agricultural programs, such as increasing the efficacy of livestock and plant breeding.

“SMRT Sequencing produces the most accurate and contiguous genome assemblies on the market, and the ultra-long range genomic connectivity of the in vivo Hi-C method serves as a perfect complement to SMRT Sequencing of large and complex genomes, helping to achieve full chromosome-level contiguity and phasing,” stated Dr. Jonas Korlach, Chief Scientific Officer at Pacific Biosciences. “Our collaboration with Phase Genomics has been truly synergistic and has yielded a method that enables researchers to get more value from long-read SMRT Sequencing and Hi-C technologies alone.”

FALCON-Phase is available as open source to scientists and also as a service through Phase Genomics. Scientists can utilize the new software to advance their current research and even revive historic genome projects with the addition of Hi-C data.

Read more about the innovative technology underpinning the new FALCON-Phase software here.

ABOUT PHASE GENOMICS – Phase Genomics applies Hi-C and other proximity-ligation methods to enable chromosome-scale genome assembly, metagenomic deconvolution, as well as analysis of structural genomic variation and genome architecture. They offer a comprehensive portfolio of laboratory and computational services and products, including Hi-C kits for plants, animals, microbes, and human samples as well as industry-leading genome and metagenome assembly and analysis software. Based in Seattle, WA, the company was founded in 2015 by a team of genome scientists, software engineers, and entrepreneurs. The company’s mission is to empower scientists with genomic tools that accelerate breakthrough discoveries.

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