Article
A diploid assembly-based benchmark for variants in the major histocompatibility complex.
Nature communications - 22 Sept 2020
Chin Chen-Shan, Wagner Justin, Zeng Qiandong, Garrison Erik, Garg Shilpa, Fungtammasan Arkarachai, Rautiainen Mikko, Aganezov Sergey, Kirsche Melanie, Zarate Samantha, Schatz Michael C, Xiao Chunlin, Rowell William J, Markello Charles, Farek Jesse, Sedlazeck Fritz J, Bansal Vikas, Yoo Byunggil, Miller Neil, Zhou Xin, Carroll Andrew, Barrio Alvaro Martinez, Salit Marc, Marschall Tobias, Dilthey Alexander T, Zook Justin M
Abstract excerpt
Most human genomes are characterized by aligning individual reads to the reference genome, but accurate long reads and linked reads now enable us to construct accurate, phased de novo assemblies. We focus on a medically important, highly variable, 5 million base-pair (bp) region where diploid assembly is particularly useful - the Major Histocompatibility Complex (MHC). Here, we develop a human genome benchmark...
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