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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-scale  de novo  genome assemblies up to nucleotide resolution. Application of AsmVar to several human  de 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 from  de novo  genome assemblies, facilitating the construction of population-scale pan-genomes. Our study also highlights the usefulness of the  de novo  assembly strategy for definition of genome structure.    Electronic supplementary material  The online version of this article (doi:10.1186/s13742-015-0103-4) contains supplementary material, which is available to authorized users.

gigascience

Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale