de novo Hybrid Assembly of the White-tailed Deer Genome

A hybrid assembly of the White-tailed deer (Odocoileus virginianus borealis) genome was generated from PacBio and Illumina reads. The New England Biolabs Ultra II DNA Library Prep Kit was used to generate a 250 bp, size-selected library from muscle tissue and paired-end sequencing (2 X 150) was performed on the Illumina NextSeq platform. A protocol modified from the PacBio SMRTbell Template Prep Kit was used to generate 10-50 kb DNA libraries from the same source material and sequencing was performed on the PacBio RSII platform. Coverage was estimated at 40X for PacBio and 150X for Illumina sequence.

Multiple assemblies were performed using FALCON 3.0, Celera Assembler 8.3, dbg2olc and Spades 3. These assemblies were compared using varying amounts of Illumina and PacBio reads across multiple parameters for each assembler. Preliminary correction of PacBio reads with Illumina reads was also examined as a potential contributor to assembly quality. We assessed the effect of “stitching” paired-end Illumina reads into a single longer read using various software methods. A novel strategy for finishing and resolution of phasing by targeted enrichment is currently underway and interim results will be presented.