De novo diploid genome assembly for genome-wide structural variant detection.

ABSTRACT: Detection of structural variants (SVs) on the basis of read alignment to a reference genome remains a difficult problem. De novo assembly, traditionally used to generate reference genomes, offers an alternative for SV detection. However, it has not been applied broadly to human genomes because of fundamental limitations of short-fragment approaches and high cost of long-read technologies. We here show that 10× linked-read sequencing supports accurate SV detection. We examined variants in six de novo 10× assemblies with diverse experimental parameters from two commonly used human cell lines: NA12878 and NA24385. The assemblies are effective for detecting mid-size SVs, which were discovered by simple pairwise alignment of the assemblies' contigs to the reference (hg38). Our stu

SUBMITTER: Zhang L 

PROVIDER: S-EPMC7671403 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature