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Monday, January 13, 2020

Direct Phased Genome Assembly Using Nighthawk on HiFi Reads

By Zev Kronenberg, Senior Engineer of Bioinformatics at PacBio   Since the introduction of HiFi reads the community has embraced these long and highly accurate reads for human genome assembly and paralog resolution [1-5]. At PacBio, the assembly team (Figure 1) is working to build on the accuracy of HiFi data for direct phasing during assembly. Figure 1. The PacBio assembly team. From left to right, James Drake, Zev Kronenberg (@ZevKronenberg), Derek Barnett (@DerekWBarnett), Chris Dunn, and Ivan Sović (@IvanSovic) In diploid organisms, phasing an assembly means separating the maternally and paternally inherited copies of each chromosome, known as haplotypes.…

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Friday, January 3, 2020

Novel Workflow Produces Fully Phased Human Genome Assemblies Without Trio Sequencing

A new preprint from lead authors David Porubsky and Peter Ebert, senior authors Evan Eichler and Tobias Marschall (@tobiasmarschal), and collaborators reports a method for generating fully phased, de novo human genome assemblies without parental data. The approach combines PacBio HiFi reads (>99% accuracy, 10-20 kb) with the short-read, single-cell Strand-seq technique.  The authors provide a proof-of-principle through assembling the genome of a Puerto Rican female from the 1000 Genomes Project. The work extends a recent publication from many of the same authors in which HiFi reads were used to produce an accurate and contiguous assembly of the human haploid…

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Monday, October 17, 2016

New FALCON Tools Enable Diploid Assemblies from SMRT Sequencing Data

In a Nature Methods paper released today, scientists describe the new bioinformatics tools to produce diploid genome assemblies from SMRT Sequencing reads. FALCON (Fast ALignment and CONsensus for assembly) and FALCON-Unzip were developed by PacBio scientists in collaboration with researchers at Johns Hopkins University, Cold Spring Harbor Laboratory, the Joint Genome Institute, and other institutions. “Phased diploid genome assembly with single-molecule real-time sequencing” comes from lead authors Chen-Shan Chin and Paul Peluso, senior author Michael Schatz, and collaborators. In the publication, the team details how FALCON and FALCON-Unzip work and presents data from several validation studies of organisms including Arabidopsis,…

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