Anchored pseudo-de novo assembly of human genomes identifies extensive sequence variation from unmapped sequence reads.

ABSTRACT: The human genome reference (HGR) completion marked the genomics era beginning, yet despite its utility universal application is limited by the small number of individuals used in its development. This is highlighted by the presence of high-quality sequence reads failing to map within the HGR. Sequences failing to map generally represent 2-5 % of total reads, which may harbor regions that would enhance our understanding of population variation, evolution, and disease. Alternatively, complete de novo assemblies can be created, but these effectively ignore the groundwork of the HGR. In an effort to find a middle ground, we developed a bioinformatic pipeline that maps paired-end reads to the HGR as separate single reads, exports unmappable reads, de novo assembles these reads per individual an

SUBMITTER: Faber-Hammond JJ 

PROVIDER: S-EPMC4899208 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature