11 human genome assemblies in 9 days
In collaboration with the genomics group at Google health, Kishwar Shafin (University of California, Santa Cruz, USA) developed a pipeline designed to identify variants from long and ultra-long reads. Capable of identifying single nucleotide variants (SNVs) in segmental duplications and regions inaccessible to short-read sequencing, the variant calling pipeline PEPPER-Margin-DeepVariant and de novo assembler Shasta present an exciting step forward for high-quality genome assembly and small variant calling. Sequencing on a PromethION and assembling the data with Shasta, eleven human genomes were successfully assembled in nine days, with SNV detection results indicating outperformance of short-read-based equivalents at the whole genome level.

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