Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Liu, Siyang; Huang, Shujia; Rao, Junhua; Ye, Weijian; Krogh, Anders; Wang, Jun
• Is Part Of: GigaScience. Volume 4:Issue 1(2015)
• Page Start: 1
• Page End: 13
• Publication Date: 2015-12
• Subjects: de novo assembly -- Structural variation -- Novel sequence; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1186/s13742-015-0103-4
• Languages: English
• ISSNs: 2047-217X

Abstract

Abstract Background Comprehensive recognition of genomic variation in one individual is important for understanding disease and developing personalized medication and treatment. Many tools based on DNA re-sequencing exist for identification of single nucleotide polymorphisms, small insertions and deletions (indels) as well as large deletions. However, these approaches consistently display a substantial bias against the recovery of complex structural variants and novel sequence in individual genomes and do not provide interpretation information such as the annotation of ancestral state and formation mechanism. Findings We present a novel approach implemented in a single software package, AsmVar, to discover, genotype and characterize different forms of structural variation and novel sequence from population-scalede novo genome assemblies up to nucleotide resolution. Application of AsmVar to several humande novo genome assemblies captures a wide spectrum of structural variants and novel sequences present in the human population in high sensitivity and specificity. Conclusions Our method provides a direct solution for investigating structural variants and novel sequences fromde novo genome assemblies, facilitating the construction of population-scale pan-genomes. Our study also highlights the usefulness of thede novo assembly strategy for definition of genome structure.