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Tool Enables Gapless Diploid Genome Assembly

National Institutes of Health scientists present this week a new software tool that enables the assembly of gapless diploid genomes. The tool, called Verkko, builds on the work of the Telomere-to-Telomere consortium, which recently assembled the first  complete human genome sequencing, relying on the manual integration of ultra-long Oxford Nanopore sequencing reads with a high-resolution assembly graph built from long, accurate PacBio high-fidelity reads. As detailed in Nature Biotechnology, Verkko starts from a multiplex de Bruijn graph built from long, accurate reads and progressively simplifies this graph by integrating ultra-long reads and haplotype-specific markers. "The result is a phased, diploid assembly of both haplotypes, with many chromosomes automatically assembled from telomere to telomere," Verkko's developers write. "With its ability to resolve complete haplotypes, Verkko ushers in a new era of comprehensive genomic analysis … [with] direct application for the construction of new reference genomes, and, ultimately, to better understanding of the relationships between large, complex structural variation, phenotype, and disease."

The Scan

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Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

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A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.